Diff for /imach/src/imach.c between versions 1.46 and 1.180

version 1.46, 2002/05/30 17:44:35 version 1.180, 2015/02/11 17:33:45
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.180  2015/02/11 17:33:45  brouard
      Summary: Finishing move from main to function (hpijx and prevalence_limit)
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.179  2015/01/04 09:57:06  brouard
   first survey ("cross") where individuals from different ages are    Summary: back to OS/X
   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 1.178  2015/01/04 09:35:48  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 1.177  2015/01/03 18:40:56  brouard
   model. More health states you consider, more time is necessary to reach the    Summary: Still testing ilc32 on OSX
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.176  2015/01/03 16:45:04  brouard
   probability to be observed in state j at the second wave    *** empty log message ***
   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 1.175  2015/01/03 16:33:42  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    *** empty log message ***
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.174  2015/01/03 16:15:49  brouard
   you to do it.  More covariates you add, slower the    Summary: Still in cross-compilation
   convergence.  
     Revision 1.173  2015/01/03 12:06:26  brouard
   The advantage of this computer programme, compared to a simple    Summary: trying to detect cross-compilation
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.172  2014/12/27 12:07:47  brouard
   intermediate interview, the information is lost, but taken into    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   account using an interpolation or extrapolation.    
     Revision 1.171  2014/12/23 13:26:59  brouard
   hPijx is the probability to be observed in state i at age x+h    Summary: Back from Visual C
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Still problem with utsname.h on Windows
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.170  2014/12/23 11:17:12  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    Summary: Cleaning some \%% back to %%
   and the contribution of each individual to the likelihood is simply  
   hPijx.    The escape was mandatory for a specific compiler (which one?), but too many warnings.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.169  2014/12/22 23:08:31  brouard
   of the life expectancies. It also computes the prevalence limits.    Summary: 0.98p
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Outputs some informations on compiler used, OS etc. Testing on different platforms.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.168  2014/12/22 15:17:42  brouard
   from the European Union.    Summary: update
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.167  2014/12/22 13:50:56  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Summary: Testing uname and compiler version and if compiled 32 or 64
   **********************************************************************/  
      Testing on Linux 64
 #include <math.h>  
 #include <stdio.h>    Revision 1.166  2014/12/22 11:40:47  brouard
 #include <stdlib.h>    *** empty log message ***
 #include <unistd.h>  
     Revision 1.165  2014/12/16 11:20:36  brouard
 #define MAXLINE 256    Summary: After compiling on Visual C
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    * imach.c (Module): Merging 1.61 to 1.162
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.164  2014/12/16 10:52:11  brouard
 #define windows    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    * imach.c (Module): Merging 1.61 to 1.162
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.163  2014/12/16 10:30:11  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    * imach.c (Module): Merging 1.61 to 1.162
   
 #define NINTERVMAX 8    Revision 1.162  2014/09/25 11:43:39  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Summary: temporary backup 0.99!
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.1  2014/09/16 11:06:58  brouard
 #define MAXN 20000    Summary: With some code (wrong) for nlopt
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Author:
 #define AGEBASE 40  
     Revision 1.161  2014/09/15 20:41:41  brouard
     Summary: Problem with macro SQR on Intel compiler
 int erreur; /* Error number */  
 int nvar;    Revision 1.160  2014/09/02 09:24:05  brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    *** empty log message ***
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.159  2014/09/01 10:34:10  brouard
 int ndeath=1; /* Number of dead states */    Summary: WIN32
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Author: Brouard
 int popbased=0;  
     Revision 1.158  2014/08/27 17:11:51  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    *** empty log message ***
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.157  2014/08/27 16:26:55  brouard
 int mle, weightopt;    Summary: Preparing windows Visual studio version
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Author: Brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    In order to compile on Visual studio, time.h is now correct and time_t
 double **oldm, **newm, **savm; /* Working pointers to matrices */    and tm struct should be used. difftime should be used but sometimes I
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    just make the differences in raw time format (time(&now).
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Trying to suppress #ifdef LINUX
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    Add xdg-open for __linux in order to open default browser.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.156  2014/08/25 20:10:10  brouard
  FILE  *ficresvij;    *** empty log message ***
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.155  2014/08/25 18:32:34  brouard
   char fileresvpl[FILENAMELENGTH];    Summary: New compile, minor changes
     Author: Brouard
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.154  2014/06/20 17:32:08  brouard
 #define FTOL 1.0e-10    Summary: Outputs now all graphs of convergence to period prevalence
   
 #define NRANSI    Revision 1.153  2014/06/20 16:45:46  brouard
 #define ITMAX 200    Summary: If 3 live state, convergence to period prevalence on same graph
     Author: Brouard
 #define TOL 2.0e-4  
     Revision 1.152  2014/06/18 17:54:09  brouard
 #define CGOLD 0.3819660    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.151  2014/06/18 16:43:30  brouard
     *** empty log message ***
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.150  2014/06/18 16:42:35  brouard
 #define TINY 1.0e-20    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
     Author: brouard
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.149  2014/06/18 15:51:14  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Summary: Some fixes in parameter files errors
      Author: Nicolas Brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.148  2014/06/17 17:38:48  brouard
     Summary: Nothing new
 static double sqrarg;    Author: Brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Just a new packaging for OS/X version 0.98nS
   
 int imx;    Revision 1.147  2014/06/16 10:33:11  brouard
 int stepm;    *** empty log message ***
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.146  2014/06/16 10:20:28  brouard
 int estepm;    Summary: Merge
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Author: Brouard
   
 int m,nb;    Merge, before building revised version.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.145  2014/06/10 21:23:15  brouard
 double **pmmij, ***probs, ***mobaverage;    Summary: Debugging with valgrind
 double dateintmean=0;    Author: Nicolas Brouard
   
 double *weight;    Lot of changes in order to output the results with some covariates
 int **s; /* Status */    After the Edimburgh REVES conference 2014, it seems mandatory to
 double *agedc, **covar, idx;    improve the code.
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    No more memory valgrind error but a lot has to be done in order to
     continue the work of splitting the code into subroutines.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Also, decodemodel has been improved. Tricode is still not
 double ftolhess; /* Tolerance for computing hessian */    optimal. nbcode should be improved. Documentation has been added in
     the source code.
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.143  2014/01/26 09:45:38  brouard
 {    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    * 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.
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.142  2014/01/26 03:57:36  brouard
 #ifdef windows    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
    s = strrchr( path, '\\' );           /* find last / */  
 #else    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    s = strrchr( path, '/' );            /* find last / */  
 #endif    Revision 1.141  2014/01/26 02:42:01  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Revision 1.140  2011/09/02 10:37:54  brouard
     Summary: times.h is ok with mingw32 now.
       if ( getwd( dirc ) == NULL ) {  
 #else    Revision 1.139  2010/06/14 07:50:17  brouard
       extern char       *getcwd( );    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
     I remember having already fixed agemin agemax which are pointers now but not cvs saved.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.138  2010/04/30 18:19:40  brouard
          return( GLOCK_ERROR_GETCWD );    *** empty log message ***
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.137  2010/04/29 18:11:38  brouard
    } else {                             /* strip direcotry from path */    (Module): Checking covariates for more complex models
       s++;                              /* after this, the filename */    than V1+V2. A lot of change to be done. Unstable.
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.136  2010/04/26 20:30:53  brouard
       strcpy( name, s );                /* save file name */    (Module): merging some libgsl code. Fixing computation
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    of likelione (using inter/intrapolation if mle = 0) in order to
       dirc[l1-l2] = 0;                  /* add zero */    get same likelihood as if mle=1.
    }    Some cleaning of code and comments added.
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    Revision 1.135  2009/10/29 15:33:14  brouard
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Revision 1.134  2009/10/29 13:18:53  brouard
 #endif    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
    s = strrchr( name, '.' );            /* find last / */  
    s++;    Revision 1.133  2009/07/06 10:21:25  brouard
    strcpy(ext,s);                       /* save extension */    just nforces
    l1= strlen( name);  
    l2= strlen( s)+1;    Revision 1.132  2009/07/06 08:22:05  brouard
    strncpy( finame, name, l1-l2);    Many tings
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    Revision 1.131  2009/06/20 16:22:47  brouard
 }    Some dimensions resccaled
   
     Revision 1.130  2009/05/26 06:44:34  brouard
 /******************************************/    (Module): Max Covariate is now set to 20 instead of 8. A
     lot of cleaning with variables initialized to 0. Trying to make
 void replace(char *s, char*t)    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 {  
   int i;    Revision 1.129  2007/08/31 13:49:27  lievre
   int lg=20;    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   i=0;  
   lg=strlen(t);    Revision 1.128  2006/06/30 13:02:05  brouard
   for(i=0; i<= lg; i++) {    (Module): Clarifications on computing e.j
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.127  2006/04/28 18:11:50  brouard
   }    (Module): Yes the sum of survivors was wrong since
 }    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
 int nbocc(char *s, char occ)    (Module): In order to speed up (in case of numerous covariates) we
 {    compute health expectancies (without variances) in a first step
   int i,j=0;    and then all the health expectancies with variances or standard
   int lg=20;    deviation (needs data from the Hessian matrices) which slows the
   i=0;    computation.
   lg=strlen(s);    In the future we should be able to stop the program is only health
   for(i=0; i<= lg; i++) {    expectancies and graph are needed without standard deviations.
   if  (s[i] == occ ) j++;  
   }    Revision 1.126  2006/04/28 17:23:28  brouard
   return j;    (Module): Yes the sum of survivors was wrong since
 }    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
 void cutv(char *u,char *v, char*t, char occ)    Version 0.98h
 {  
   int i,lg,j,p=0;    Revision 1.125  2006/04/04 15:20:31  lievre
   i=0;    Errors in calculation of health expectancies. Age was not initialized.
   for(j=0; j<=strlen(t)-1; j++) {    Forecasting file added.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Revision 1.124  2006/03/22 17:13:53  lievre
     Parameters are printed with %lf instead of %f (more numbers after the comma).
   lg=strlen(t);    The log-likelihood is printed in the log file
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    Revision 1.123  2006/03/20 10:52:43  brouard
   }    * imach.c (Module): <title> changed, corresponds to .htm file
      u[p]='\0';    name. <head> headers where missing.
   
    for(j=0; j<= lg; j++) {    * imach.c (Module): Weights can have a decimal point as for
     if (j>=(p+1))(v[j-p-1] = t[j]);    English (a comma might work with a correct LC_NUMERIC environment,
   }    otherwise the weight is truncated).
 }    Modification of warning when the covariates values are not 0 or
     1.
 /********************** nrerror ********************/    Version 0.98g
   
 void nrerror(char error_text[])    Revision 1.122  2006/03/20 09:45:41  brouard
 {    (Module): Weights can have a decimal point as for
   fprintf(stderr,"ERREUR ...\n");    English (a comma might work with a correct LC_NUMERIC environment,
   fprintf(stderr,"%s\n",error_text);    otherwise the weight is truncated).
   exit(1);    Modification of warning when the covariates values are not 0 or
 }    1.
 /*********************** vector *******************/    Version 0.98g
 double *vector(int nl, int nh)  
 {    Revision 1.121  2006/03/16 17:45:01  lievre
   double *v;    * imach.c (Module): Comments concerning covariates added
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    * imach.c (Module): refinements in the computation of lli if
   return v-nl+NR_END;    status=-2 in order to have more reliable computation if stepm is
 }    not 1 month. Version 0.98f
   
 /************************ free vector ******************/    Revision 1.120  2006/03/16 15:10:38  lievre
 void free_vector(double*v, int nl, int nh)    (Module): refinements in the computation of lli if
 {    status=-2 in order to have more reliable computation if stepm is
   free((FREE_ARG)(v+nl-NR_END));    not 1 month. Version 0.98f
 }  
     Revision 1.119  2006/03/15 17:42:26  brouard
 /************************ivector *******************************/    (Module): Bug if status = -2, the loglikelihood was
 int *ivector(long nl,long nh)    computed as likelihood omitting the logarithm. Version O.98e
 {  
   int *v;    Revision 1.118  2006/03/14 18:20:07  brouard
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    (Module): varevsij Comments added explaining the second
   if (!v) nrerror("allocation failure in ivector");    table of variances if popbased=1 .
   return v-nl+NR_END;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 }    (Module): Function pstamp added
     (Module): Version 0.98d
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    Revision 1.117  2006/03/14 17:16:22  brouard
 {    (Module): varevsij Comments added explaining the second
   free((FREE_ARG)(v+nl-NR_END));    table of variances if popbased=1 .
 }    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 /******************* imatrix *******************************/    (Module): Version 0.98d
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Revision 1.116  2006/03/06 10:29:27  brouard
 {    (Module): Variance-covariance wrong links and
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    varian-covariance of ej. is needed (Saito).
   int **m;  
      Revision 1.115  2006/02/27 12:17:45  brouard
   /* allocate pointers to rows */    (Module): One freematrix added in mlikeli! 0.98c
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.114  2006/02/26 12:57:58  brouard
   m += NR_END;    (Module): Some improvements in processing parameter
   m -= nrl;    filename with strsep.
    
      Revision 1.113  2006/02/24 14:20:24  brouard
   /* allocate rows and set pointers to them */    (Module): Memory leaks checks with valgrind and:
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    datafile was not closed, some imatrix were not freed and on matrix
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    allocation too.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.112  2006/01/30 09:55:26  brouard
      (Module): Back to gnuplot.exe instead of wgnuplot.exe
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
      Revision 1.111  2006/01/25 20:38:18  brouard
   /* return pointer to array of pointers to rows */    (Module): Lots of cleaning and bugs added (Gompertz)
   return m;    (Module): Comments can be added in data file. Missing date values
 }    can be a simple dot '.'.
   
 /****************** free_imatrix *************************/    Revision 1.110  2006/01/25 00:51:50  brouard
 void free_imatrix(m,nrl,nrh,ncl,nch)    (Module): Lots of cleaning and bugs added (Gompertz)
       int **m;  
       long nch,ncl,nrh,nrl;    Revision 1.109  2006/01/24 19:37:15  brouard
      /* free an int matrix allocated by imatrix() */    (Module): Comments (lines starting with a #) are allowed in data.
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    Revision 1.108  2006/01/19 18:05:42  lievre
   free((FREE_ARG) (m+nrl-NR_END));    Gnuplot problem appeared...
 }    To be fixed
   
 /******************* matrix *******************************/    Revision 1.107  2006/01/19 16:20:37  brouard
 double **matrix(long nrl, long nrh, long ncl, long nch)    Test existence of gnuplot in imach path
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    Revision 1.106  2006/01/19 13:24:36  brouard
   double **m;    Some cleaning and links added in html output
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.105  2006/01/05 20:23:19  lievre
   if (!m) nrerror("allocation failure 1 in matrix()");    *** empty log message ***
   m += NR_END;  
   m -= nrl;    Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): If the status is missing at the last wave but we know
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    that the person is alive, then we can code his/her status as -2
   m[nrl] += NR_END;    (instead of missing=-1 in earlier versions) and his/her
   m[nrl] -= ncl;    contributions to the likelihood is 1 - Prob of dying from last
     health status (= 1-p13= p11+p12 in the easiest case of somebody in
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    the healthy state at last known wave). Version is 0.98
   return m;  
 }    Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    Revision 1.102  2004/09/15 17:31:30  brouard
 {    Add the possibility to read data file including tab characters.
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    Revision 1.101  2004/09/15 10:38:38  brouard
 }    Fix on curr_time
   
 /******************* ma3x *******************************/    Revision 1.100  2004/07/12 18:29:06  brouard
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Add version for Mac OS X. Just define UNIX in Makefile
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Revision 1.99  2004/06/05 08:57:40  brouard
   double ***m;    *** empty log message ***
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.98  2004/05/16 15:05:56  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    New version 0.97 . First attempt to estimate force of mortality
   m += NR_END;    directly from the data i.e. without the need of knowing the health
   m -= nrl;    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
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    other analysis, in order to test if the mortality estimated from the
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    cross-longitudinal survey is different from the mortality estimated
   m[nrl] += NR_END;    from other sources like vital statistic data.
   m[nrl] -= ncl;  
     The same imach parameter file can be used but the option for mle should be -3.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
     Agnès, who wrote this part of the code, tried to keep most of the
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    former routines in order to include the new code within the former code.
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;    The output is very simple: only an estimate of the intercept and of
   m[nrl][ncl] -= nll;    the slope with 95% confident intervals.
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;    Current limitations:
      A) Even if you enter covariates, i.e. with the
   for (i=nrl+1; i<=nrh; i++) {    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    B) There is no computation of Life Expectancy nor Life Table.
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;    Revision 1.97  2004/02/20 13:25:42  lievre
   }    Version 0.96d. Population forecasting command line is (temporarily)
   return m;    suppressed.
 }  
     Revision 1.96  2003/07/15 15:38:55  brouard
 /*************************free ma3x ************************/    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    rewritten within the same printf. Workaround: many printfs.
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    Revision 1.95  2003/07/08 07:54:34  brouard
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    * imach.c (Repository):
   free((FREE_ARG)(m+nrl-NR_END));    (Repository): Using imachwizard code to output a more meaningful covariance
 }    matrix (cov(a12,c31) instead of numbers.
   
 /***************** f1dim *************************/    Revision 1.94  2003/06/27 13:00:02  brouard
 extern int ncom;    Just cleaning
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);    Revision 1.93  2003/06/25 16:33:55  brouard
      (Module): On windows (cygwin) function asctime_r doesn't
 double f1dim(double x)    exist so I changed back to asctime which exists.
 {    (Module): Version 0.96b
   int j;  
   double f;    Revision 1.92  2003/06/25 16:30:45  brouard
   double *xt;    (Module): On windows (cygwin) function asctime_r doesn't
      exist so I changed back to asctime which exists.
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    Revision 1.91  2003/06/25 15:30:29  brouard
   f=(*nrfunc)(xt);    * imach.c (Repository): Duplicated warning errors corrected.
   free_vector(xt,1,ncom);    (Repository): Elapsed time after each iteration is now output. It
   return f;    helps to forecast when convergence will be reached. Elapsed time
 }    is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    Revision 1.90  2003/06/24 12:34:15  brouard
 {    (Module): Some bugs corrected for windows. Also, when
   int iter;    mle=-1 a template is output in file "or"mypar.txt with the design
   double a,b,d,etemp;    of the covariance matrix to be input.
   double fu,fv,fw,fx;  
   double ftemp;    Revision 1.89  2003/06/24 12:30:52  brouard
   double p,q,r,tol1,tol2,u,v,w,x,xm;    (Module): Some bugs corrected for windows. Also, when
   double e=0.0;    mle=-1 a template is output in file "or"mypar.txt with the design
      of the covariance matrix to be input.
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);    Revision 1.88  2003/06/23 17:54:56  brouard
   x=w=v=bx;    * 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.
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {    Revision 1.87  2003/06/18 12:26:01  brouard
     xm=0.5*(a+b);    Version 0.96
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    Revision 1.86  2003/06/17 20:04:08  brouard
     printf(".");fflush(stdout);    (Module): Change position of html and gnuplot routines and added
 #ifdef DEBUG    routine fileappend.
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    Revision 1.85  2003/06/17 13:12:43  brouard
 #endif    * imach.c (Repository): Check when date of death was earlier that
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    current date of interview. It may happen when the death was just
       *xmin=x;    prior to the death. In this case, dh was negative and likelihood
       return fx;    was wrong (infinity). We still send an "Error" but patch by
     }    assuming that the date of death was just one stepm after the
     ftemp=fu;    interview.
     if (fabs(e) > tol1) {    (Repository): Because some people have very long ID (first column)
       r=(x-w)*(fx-fv);    we changed int to long in num[] and we added a new lvector for
       q=(x-v)*(fx-fw);    memory allocation. But we also truncated to 8 characters (left
       p=(x-v)*q-(x-w)*r;    truncation)
       q=2.0*(q-r);    (Repository): No more line truncation errors.
       if (q > 0.0) p = -p;  
       q=fabs(q);    Revision 1.84  2003/06/13 21:44:43  brouard
       etemp=e;    * imach.c (Repository): Replace "freqsummary" at a correct
       e=d;    place. It differs from routine "prevalence" which may be called
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    many times. Probs is memory consuming and must be used with
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    parcimony.
       else {    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
         d=p/q;  
         u=x+d;    Revision 1.83  2003/06/10 13:39:11  lievre
         if (u-a < tol2 || b-u < tol2)    *** empty log message ***
           d=SIGN(tol1,xm-x);  
       }    Revision 1.82  2003/06/05 15:57:20  brouard
     } else {    Add log in  imach.c and  fullversion number is now printed.
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  /*
     fu=(*f)(u);     Interpolated Markov Chain
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;    Short summary of the programme:
       SHFT(v,w,x,u)    
         SHFT(fv,fw,fx,fu)    This program computes Healthy Life Expectancies from
         } else {    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
           if (u < x) a=u; else b=u;    first survey ("cross") where individuals from different ages are
           if (fu <= fw || w == x) {    interviewed on their health status or degree of disability (in the
             v=w;    case of a health survey which is our main interest) -2- at least a
             w=u;    second wave of interviews ("longitudinal") which measure each change
             fv=fw;    (if any) in individual health status.  Health expectancies are
             fw=fu;    computed from the time spent in each health state according to a
           } else if (fu <= fv || v == x || v == w) {    model. More health states you consider, more time is necessary to reach the
             v=u;    Maximum Likelihood of the parameters involved in the model.  The
             fv=fu;    simplest model is the multinomial logistic model where pij is the
           }    probability to be observed in state j at the second wave
         }    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
   nrerror("Too many iterations in brent");    'age' is age and 'sex' is a covariate. If you want to have a more
   *xmin=x;    complex model than "constant and age", you should modify the program
   return fx;    where the markup *Covariates have to be included here again* invites
 }    you to do it.  More covariates you add, slower the
     convergence.
 /****************** mnbrak ***********************/  
     The advantage of this computer programme, compared to a simple
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    multinomial logistic model, is clear when the delay between waves is not
             double (*func)(double))    identical for each individual. Also, if a individual missed an
 {    intermediate interview, the information is lost, but taken into
   double ulim,u,r,q, dum;    account using an interpolation or extrapolation.  
   double fu;  
      hPijx is the probability to be observed in state i at age x+h
   *fa=(*func)(*ax);    conditional to the observed state i at age x. The delay 'h' can be
   *fb=(*func)(*bx);    split into an exact number (nh*stepm) of unobserved intermediate
   if (*fb > *fa) {    states. This elementary transition (by month, quarter,
     SHFT(dum,*ax,*bx,dum)    semester or year) is modelled as a multinomial logistic.  The hPx
       SHFT(dum,*fb,*fa,dum)    matrix is simply the matrix product of nh*stepm elementary matrices
       }    and the contribution of each individual to the likelihood is simply
   *cx=(*bx)+GOLD*(*bx-*ax);    hPijx.
   *fc=(*func)(*cx);  
   while (*fb > *fc) {    Also this programme outputs the covariance matrix of the parameters but also
     r=(*bx-*ax)*(*fb-*fc);    of the life expectancies. It also computes the period (stable) prevalence. 
     q=(*bx-*cx)*(*fb-*fa);    
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));             Institut national d'études démographiques, Paris.
     ulim=(*bx)+GLIMIT*(*cx-*bx);    This software have been partly granted by Euro-REVES, a concerted action
     if ((*bx-u)*(u-*cx) > 0.0) {    from the European Union.
       fu=(*func)(u);    It is copyrighted identically to a GNU software product, ie programme and
     } else if ((*cx-u)*(u-ulim) > 0.0) {    software can be distributed freely for non commercial use. Latest version
       fu=(*func)(u);    can be accessed at http://euroreves.ined.fr/imach .
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
           SHFT(*fb,*fc,fu,(*func)(u))    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
           }    
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    **********************************************************************/
       u=ulim;  /*
       fu=(*func)(u);    main
     } else {    read parameterfile
       u=(*cx)+GOLD*(*cx-*bx);    read datafile
       fu=(*func)(u);    concatwav
     }    freqsummary
     SHFT(*ax,*bx,*cx,u)    if (mle >= 1)
       SHFT(*fa,*fb,*fc,fu)      mlikeli
       }    print results files
 }    if mle==1 
        computes hessian
 /*************** linmin ************************/    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 int ncom;    open gnuplot file
 double *pcom,*xicom;    open html file
 double (*nrfunc)(double []);    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
       for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
 {      freexexit2 possible for memory heap.
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);    h Pij x                         | pij_nom  ficrestpij
   double f1dim(double x);     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
               double *fc, double (*func)(double));         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   int j;  
   double xx,xmin,bx,ax;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   double fx,fb,fa;         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 ()
   ncom=n;     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   pcom=vector(1,n);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   xicom=vector(1,n);  
   nrfunc=func;    forecasting if prevfcast==1 prevforecast call prevalence()
   for (j=1;j<=n;j++) {    health expectancies
     pcom[j]=p[j];    Variance-covariance of DFLE
     xicom[j]=xi[j];    prevalence()
   }     movingaverage()
   ax=0.0;    varevsij() 
   xx=1.0;    if popbased==1 varevsij(,popbased)
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    total life expectancies
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    Variance of period (stable) prevalence
 #ifdef DEBUG   end
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  */
 #endif  
   for (j=1;j<=n;j++) {  #define POWELL /* Instead of NLOPT */
     xi[j] *= xmin;  
     p[j] += xi[j];  #include <math.h>
   }  #include <stdio.h>
   free_vector(xicom,1,n);  #include <stdlib.h>
   free_vector(pcom,1,n);  #include <string.h>
 }  
   #ifdef _WIN32
 /*************** powell ************************/  #include <io.h>
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #include <windows.h>
             double (*func)(double []))  #include <tchar.h>
 {  #else
   void linmin(double p[], double xi[], int n, double *fret,  #include <unistd.h>
               double (*func)(double []));  #endif
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  #include <limits.h>
   double fp,fptt;  #include <sys/types.h>
   double *xits;  
   pt=vector(1,n);  #if defined(__GNUC__)
   ptt=vector(1,n);  #include <sys/utsname.h> /* Doesn't work on Windows */
   xit=vector(1,n);  #endif
   xits=vector(1,n);  
   *fret=(*func)(p);  #include <sys/stat.h>
   for (j=1;j<=n;j++) pt[j]=p[j];  #include <errno.h>
   for (*iter=1;;++(*iter)) {  /* extern int errno; */
     fp=(*fret);  
     ibig=0;  /* #ifdef LINUX */
     del=0.0;  /* #include <time.h> */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /* #include "timeval.h" */
     for (i=1;i<=n;i++)  /* #else */
       printf(" %d %.12f",i, p[i]);  /* #include <sys/time.h> */
     printf("\n");  /* #endif */
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  #include <time.h>
       fptt=(*fret);  
 #ifdef DEBUG  #ifdef GSL
       printf("fret=%lf \n",*fret);  #include <gsl/gsl_errno.h>
 #endif  #include <gsl/gsl_multimin.h>
       printf("%d",i);fflush(stdout);  #endif
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  
         del=fabs(fptt-(*fret));  #ifdef NLOPT
         ibig=i;  #include <nlopt.h>
       }  typedef struct {
 #ifdef DEBUG    double (* function)(double [] );
       printf("%d %.12e",i,(*fret));  } myfunc_data ;
       for (j=1;j<=n;j++) {  #endif
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  /* #include <libintl.h> */
       }  /* #define _(String) gettext (String) */
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       printf("\n");  
 #endif  #define GNUPLOTPROGRAM "gnuplot"
     }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #define FILENAMELENGTH 132
 #ifdef DEBUG  
       int k[2],l;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       k[0]=1;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
       for (j=1;j<=n;j++)  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
         printf(" %.12e",p[j]);  
       printf("\n");  #define NINTERVMAX 8
       for(l=0;l<=1;l++) {  #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) */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
         }  #define MAXN 20000
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  #define YEARM 12. /**< Number of months per year */
       }  #define AGESUP 130
 #endif  #define AGEBASE 40
   #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
   #ifdef _WIN32
       free_vector(xit,1,n);  #define DIRSEPARATOR '\\'
       free_vector(xits,1,n);  #define CHARSEPARATOR "\\"
       free_vector(ptt,1,n);  #define ODIRSEPARATOR '/'
       free_vector(pt,1,n);  #else
       return;  #define DIRSEPARATOR '/'
     }  #define CHARSEPARATOR "/"
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #define ODIRSEPARATOR '\\'
     for (j=1;j<=n;j++) {  #endif
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];  /* $Id$ */
       pt[j]=p[j];  /* $State$ */
     }  
     fptt=(*func)(ptt);  char version[]="Imach version 0.98p, Février 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
     if (fptt < fp) {  char fullversion[]="$Revision$ $Date$"; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  char strstart[80];
       if (t < 0.0) {  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
         linmin(p,xit,n,fret,func);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
         for (j=1;j<=n;j++) {  int nvar=0, nforce=0; /* Number of variables, number of forces */
           xi[j][ibig]=xi[j][n];  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
           xi[j][n]=xit[j];  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
         }  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
 #ifdef DEBUG  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
         for(j=1;j<=n;j++)  int cptcovprodnoage=0; /**< Number of covariate products without age */   
           printf(" %.12e",xit[j]);  int cptcoveff=0; /* Total number of covariates to vary for printing results */
         printf("\n");  int cptcov=0; /* Working variable */
 #endif  int npar=NPARMAX;
       }  int nlstate=2; /* Number of live states */
     }  int ndeath=1; /* Number of dead states */
   }  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 }  int popbased=0;
   
 /**** Prevalence limit ****************/  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav=0; /* Maxim number of waves */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
 {  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
      matrix by transitions matrix until convergence is reached */                     to the likelihood and the sum of weights (done by funcone)*/
   int mle=1, weightopt=0;
   int i, ii,j,k;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   double min, max, maxmin, maxmax,sumnew=0.;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   double **matprod2();  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   double **out, cov[NCOVMAX], **pmij();             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double **newm;  int countcallfunc=0;  /* Count the number of calls to func */
   double agefin, delaymax=50 ; /* Max number of years to converge */  double jmean=1; /* Mean space between 2 waves */
   double **matprod2(); /* test */
   for (ii=1;ii<=nlstate+ndeath;ii++)  double **oldm, **newm, **savm; /* Working pointers to matrices */
     for (j=1;j<=nlstate+ndeath;j++){  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /*FILE *fic ; */ /* Used in readdata only */
     }  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
    cov[1]=1.;  int globpr=0; /* Global variable for printing or not */
    double fretone; /* Only one call to likelihood */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  long ipmx=0; /* Number of contributions */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  double sw; /* Sum of weights */
     newm=savm;  char filerespow[FILENAMELENGTH];
     /* Covariates have to be included here again */  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
      cov[2]=agefin;  FILE *ficresilk;
    FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       for (k=1; k<=cptcovn;k++) {  FILE *ficresprobmorprev;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  FILE *fichtm, *fichtmcov; /* Html File */
         /*      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]]);*/  FILE *ficreseij;
       }  char filerese[FILENAMELENGTH];
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  FILE *ficresstdeij;
       for (k=1; k<=cptcovprod;k++)  char fileresstde[FILENAMELENGTH];
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  FILE *ficrescveij;
   char filerescve[FILENAMELENGTH];
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  FILE  *ficresvij;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  char fileresv[FILENAMELENGTH];
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  FILE  *ficresvpl;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
     savm=oldm;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     oldm=newm;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     maxmax=0.;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     for(j=1;j<=nlstate;j++){  char command[FILENAMELENGTH];
       min=1.;  int  outcmd=0;
       max=0.;  
       for(i=1; i<=nlstate; i++) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  char filelog[FILENAMELENGTH]; /* Log file */
         prlim[i][j]= newm[i][j]/(1-sumnew);  char filerest[FILENAMELENGTH];
         max=FMAX(max,prlim[i][j]);  char fileregp[FILENAMELENGTH];
         min=FMIN(min,prlim[i][j]);  char popfile[FILENAMELENGTH];
       }  
       maxmin=max-min;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       maxmax=FMAX(maxmax,maxmin);  
     }  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
     if(maxmax < ftolpl){  /* struct timezone tzp; */
       return prlim;  /* extern int gettimeofday(); */
     }  struct tm tml, *gmtime(), *localtime();
   }  
 }  extern time_t time();
   
 /*************** transition probabilities ***************/  struct tm start_time, end_time, curr_time, last_time, forecast_time;
   time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  struct tm tm;
 {  
   double s1, s2;  char strcurr[80], strfor[80];
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;  char *endptr;
   long lval;
     for(i=1; i<= nlstate; i++){  double dval;
     for(j=1; j<i;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #define NR_END 1
         /*s2 += param[i][j][nc]*cov[nc];*/  #define FREE_ARG char*
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  #define FTOL 1.0e-10
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  #define NRANSI 
       ps[i][j]=s2;  #define ITMAX 200 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  #define TOL 2.0e-4 
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #define CGOLD 0.3819660 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  #define ZEPS 1.0e-10 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       }  
       ps[i][j]=s2;  #define GOLD 1.618034 
     }  #define GLIMIT 100.0 
   }  #define TINY 1.0e-20 
     /*ps[3][2]=1;*/  
   static double maxarg1,maxarg2;
   for(i=1; i<= nlstate; i++){  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
      s1=0;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     for(j=1; j<i; j++)    
       s1+=exp(ps[i][j]);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     for(j=i+1; j<=nlstate+ndeath; j++)  #define rint(a) floor(a+0.5)
       s1+=exp(ps[i][j]);  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
     ps[i][i]=1./(s1+1.);  /* #define mytinydouble 1.0e-16 */
     for(j=1; j<i; j++)  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /* 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; */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  static double sqrarg;
   } /* end i */  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  int agegomp= AGEGOMP;
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  int imx; 
       ps[ii][ii]=1;  int stepm=1;
     }  /* Stepm, step in month: minimum step interpolation*/
   }  
   int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  int m,nb;
      printf("%lf ",ps[ii][jj]);  long *num;
    }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     printf("\n ");  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     }  double **pmmij, ***probs;
     printf("\n ");printf("%lf ",cov[2]);*/  double *ageexmed,*agecens;
 /*  double dateintmean=0;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  
   goto end;*/  double *weight;
     return ps;  int **s; /* Status */
 }  double *agedc;
   double  **covar; /**< covar[j,i], value of jth covariate for individual i,
 /**************** Product of 2 matrices ******************/                    * covar=matrix(0,NCOVMAX,1,n); 
                     * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  double  idx; 
 {  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  int *Ndum; /** Freq of modality (tricode */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   /* in, b, out are matrice of pointers which should have been initialized  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
      before: only the contents of out is modified. The function returns  double *lsurv, *lpop, *tpop;
      a pointer to pointers identical to out */  
   long i, j, k;  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   for(i=nrl; i<= nrh; i++)  double ftolhess; /**< Tolerance for computing hessian */
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  /**************** split *************************/
         out[i][k] +=in[i][j]*b[j][k];  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
   return out;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 }       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     */ 
     char  *ss;                            /* pointer */
 /************* Higher Matrix Product ***************/    int   l1, l2;                         /* length counters */
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    l1 = strlen(path );                   /* length of path */
 {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
      duration (i.e. until    if ( ss == NULL ) {                   /* no directory, so determine current directory */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      strcpy( name, path );               /* we got the fullname name because no directory */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
      (typically every 2 years instead of every month which is too big).        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      Model is determined by parameters x and covariates have to be      /* get current working directory */
      included manually here.      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
      */        return( GLOCK_ERROR_GETCWD );
       }
   int i, j, d, h, k;      /* got dirc from getcwd*/
   double **out, cov[NCOVMAX];      printf(" DIRC = %s \n",dirc);
   double **newm;    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
   /* Hstepm could be zero and should return the unit matrix */      l2 = strlen( ss );                  /* length of filename */
   for (i=1;i<=nlstate+ndeath;i++)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     for (j=1;j<=nlstate+ndeath;j++){      strcpy( name, ss );         /* save file name */
       oldm[i][j]=(i==j ? 1.0 : 0.0);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       po[i][j][0]=(i==j ? 1.0 : 0.0);      dirc[l1-l2] = 0;                    /* add zero */
     }      printf(" DIRC2 = %s \n",dirc);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    }
   for(h=1; h <=nhstepm; h++){    /* We add a separator at the end of dirc if not exists */
     for(d=1; d <=hstepm; d++){    l1 = strlen( dirc );                  /* length of directory */
       newm=savm;    if( dirc[l1-1] != DIRSEPARATOR ){
       /* Covariates have to be included here again */      dirc[l1] =  DIRSEPARATOR;
       cov[1]=1.;      dirc[l1+1] = 0; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      printf(" DIRC3 = %s \n",dirc);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    }
       for (k=1; k<=cptcovage;k++)    ss = strrchr( name, '.' );            /* find last / */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    if (ss >0){
       for (k=1; k<=cptcovprod;k++)      ss++;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
       l2= strlen(ss)+1;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      strncpy( finame, name, l1-l2);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      finame[l1-l2]= 0;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;    return( 0 );                          /* we're done */
       oldm=newm;  }
     }  
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {  /******************************************/
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  void replace_back_to_slash(char *s, char*t)
          */  {
       }    int i;
   } /* end h */    int lg=0;
   return po;    i=0;
 }    lg=strlen(t);
     for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
 /*************** log-likelihood *************/      if (t[i]== '\\') s[i]='/';
 double func( double *x)    }
 {  }
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  char *trimbb(char *out, char *in)
   double **out;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
   double sw; /* Sum of weights */    char *s;
   double lli; /* Individual log likelihood */    s=out;
   long ipmx;    while (*in != '\0'){
   /*extern weight */      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   /* We are differentiating ll according to initial status */        in++;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      }
   /*for(i=1;i<imx;i++)      *out++ = *in++;
     printf(" %d\n",s[4][i]);    }
   */    *out='\0';
   cov[1]=1.;    return s;
   }
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  char *cutl(char *blocc, char *alocc, char *in, char occ)
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  {
     for(mi=1; mi<= wav[i]-1; mi++){    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
       for (ii=1;ii<=nlstate+ndeath;ii++)       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);       gives blocc="abcdef2ghi" and alocc="j".
       for(d=0; d<dh[mi][i]; d++){       If occ is not found blocc is null and alocc is equal to in. Returns blocc
         newm=savm;    */
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    char *s, *t;
         for (kk=1; kk<=cptcovage;kk++) {    t=in;s=in;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    while ((*in != occ) && (*in != '\0')){
         }      *alocc++ = *in++;
            }
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    if( *in == occ){
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      *(alocc)='\0';
         savm=oldm;      s=++in;
         oldm=newm;    }
           
            if (s == t) {/* occ not found */
       } /* end mult */      *(alocc-(in-s))='\0';
            in=s;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    }
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    while ( *in != '\0'){
       ipmx +=1;      *blocc++ = *in++;
       sw += weight[i];    }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */    *blocc='\0';
   } /* end of individual */    return t;
   }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  char *cutv(char *blocc, char *alocc, char *in, char occ)
   /* 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 */    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
   return -l;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
 }       gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns alocc
     */
 /*********** Maximum Likelihood Estimation ***************/    char *s, *t;
     t=in;s=in;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    while (*in != '\0'){
 {      while( *in == occ){
   int i,j, iter;        *blocc++ = *in++;
   double **xi,*delti;        s=in;
   double fret;      }
   xi=matrix(1,npar,1,npar);      *blocc++ = *in++;
   for (i=1;i<=npar;i++)    }
     for (j=1;j<=npar;j++)    if (s == t) /* occ not found */
       xi[i][j]=(i==j ? 1.0 : 0.0);      *(blocc-(in-s))='\0';
   printf("Powell\n");    else
   powell(p,xi,npar,ftol,&iter,&fret,func);      *(blocc-(in-s)-1)='\0';
     in=s;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    while ( *in != '\0'){
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      *alocc++ = *in++;
     }
 }  
     *alocc='\0';
 /**** Computes Hessian and covariance matrix ***/    return s;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  }
 {  
   double  **a,**y,*x,pd;  int nbocc(char *s, char occ)
   double **hess;  {
   int i, j,jk;    int i,j=0;
   int *indx;    int lg=20;
     i=0;
   double hessii(double p[], double delta, int theta, double delti[]);    lg=strlen(s);
   double hessij(double p[], double delti[], int i, int j);    for(i=0; i<= lg; i++) {
   void lubksb(double **a, int npar, int *indx, double b[]) ;    if  (s[i] == occ ) j++;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    }
     return j;
   hess=matrix(1,npar,1,npar);  }
   
   printf("\nCalculation of the hessian matrix. Wait...\n");  /* void cutv(char *u,char *v, char*t, char occ) */
   for (i=1;i<=npar;i++){  /* { */
     printf("%d",i);fflush(stdout);  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
     hess[i][i]=hessii(p,ftolhess,i,delti);  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     /*printf(" %f ",p[i]);*/  /*      gives u="abcdef2ghi" and v="j" *\/ */
     /*printf(" %lf ",hess[i][i]);*/  /*   int i,lg,j,p=0; */
   }  /*   i=0; */
    /*   lg=strlen(t); */
   for (i=1;i<=npar;i++) {  /*   for(j=0; j<=lg-1; j++) { */
     for (j=1;j<=npar;j++)  {  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
       if (j>i) {  /*   } */
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);  /*   for(j=0; j<p; j++) { */
         hess[j][i]=hess[i][j];      /*     (u[j] = t[j]); */
         /*printf(" %lf ",hess[i][j]);*/  /*   } */
       }  /*      u[p]='\0'; */
     }  
   }  /*    for(j=0; j<= lg; j++) { */
   printf("\n");  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /*   } */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  /* } */
    
   a=matrix(1,npar,1,npar);  #ifdef _WIN32
   y=matrix(1,npar,1,npar);  char * strsep(char **pp, const char *delim)
   x=vector(1,npar);  {
   indx=ivector(1,npar);    char *p, *q;
   for (i=1;i<=npar;i++)           
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    if ((p = *pp) == NULL)
   ludcmp(a,npar,indx,&pd);      return 0;
     if ((q = strpbrk (p, delim)) != NULL)
   for (j=1;j<=npar;j++) {    {
     for (i=1;i<=npar;i++) x[i]=0;      *pp = q + 1;
     x[j]=1;      *q = '\0';
     lubksb(a,npar,indx,x);    }
     for (i=1;i<=npar;i++){    else
       matcov[i][j]=x[i];      *pp = 0;
     }    return p;
   }  }
   #endif
   printf("\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {  /********************** nrerror ********************/
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);  void nrerror(char error_text[])
     }  {
     printf("\n");    fprintf(stderr,"ERREUR ...\n");
   }    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
   /* Recompute Inverse */  }
   for (i=1;i<=npar;i++)  /*********************** vector *******************/
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  double *vector(int nl, int nh)
   ludcmp(a,npar,indx,&pd);  {
     double *v;
   /*  printf("\n#Hessian matrix recomputed#\n");    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
   for (j=1;j<=npar;j++) {    return v-nl+NR_END;
     for (i=1;i<=npar;i++) x[i]=0;  }
     x[j]=1;  
     lubksb(a,npar,indx,x);  /************************ free vector ******************/
     for (i=1;i<=npar;i++){  void free_vector(double*v, int nl, int nh)
       y[i][j]=x[i];  {
       printf("%.3e ",y[i][j]);    free((FREE_ARG)(v+nl-NR_END));
     }  }
     printf("\n");  
   }  /************************ivector *******************************/
   */  int *ivector(long nl,long nh)
   {
   free_matrix(a,1,npar,1,npar);    int *v;
   free_matrix(y,1,npar,1,npar);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   free_vector(x,1,npar);    if (!v) nrerror("allocation failure in ivector");
   free_ivector(indx,1,npar);    return v-nl+NR_END;
   free_matrix(hess,1,npar,1,npar);  }
   
   /******************free ivector **************************/
 }  void free_ivector(int *v, long nl, long nh)
   {
 /*************** hessian matrix ****************/    free((FREE_ARG)(v+nl-NR_END));
 double hessii( double x[], double delta, int theta, double delti[])  }
 {  
   int i;  /************************lvector *******************************/
   int l=1, lmax=20;  long *lvector(long nl,long nh)
   double k1,k2;  {
   double p2[NPARMAX+1];    long *v;
   double res;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    if (!v) nrerror("allocation failure in ivector");
   double fx;    return v-nl+NR_END;
   int k=0,kmax=10;  }
   double l1;  
   /******************free lvector **************************/
   fx=func(x);  void free_lvector(long *v, long nl, long nh)
   for (i=1;i<=npar;i++) p2[i]=x[i];  {
   for(l=0 ; l <=lmax; l++){    free((FREE_ARG)(v+nl-NR_END));
     l1=pow(10,l);  }
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){  /******************* imatrix *******************************/
       delt = delta*(l1*k);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       p2[theta]=x[theta] +delt;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       k1=func(p2)-fx;  { 
       p2[theta]=x[theta]-delt;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       k2=func(p2)-fx;    int **m; 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    /* allocate pointers to rows */ 
          m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 #ifdef DEBUG    if (!m) nrerror("allocation failure 1 in matrix()"); 
       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);    m += NR_END; 
 #endif    m -= nrl; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    
         k=kmax;    /* allocate rows and set pointers to them */ 
       }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         k=kmax; l=lmax*10.;    m[nrl] += NR_END; 
       }    m[nrl] -= ncl; 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    
         delts=delt;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       }    
     }    /* return pointer to array of pointers to rows */ 
   }    return m; 
   delti[theta]=delts;  } 
   return res;  
    /****************** free_imatrix *************************/
 }  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
 double hessij( double x[], double delti[], int thetai,int thetaj)        long nch,ncl,nrh,nrl; 
 {       /* free an int matrix allocated by imatrix() */ 
   int i;  { 
   int l=1, l1, lmax=20;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   double k1,k2,k3,k4,res,fx;    free((FREE_ARG) (m+nrl-NR_END)); 
   double p2[NPARMAX+1];  } 
   int k;  
   /******************* matrix *******************************/
   fx=func(x);  double **matrix(long nrl, long nrh, long ncl, long nch)
   for (k=1; k<=2; k++) {  {
     for (i=1;i<=npar;i++) p2[i]=x[i];    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     p2[thetai]=x[thetai]+delti[thetai]/k;    double **m;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
      if (!m) nrerror("allocation failure 1 in matrix()");
     p2[thetai]=x[thetai]+delti[thetai]/k;    m += NR_END;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    m -= nrl;
     k2=func(p2)-fx;  
      m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     p2[thetai]=x[thetai]-delti[thetai]/k;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    m[nrl] += NR_END;
     k3=func(p2)-fx;    m[nrl] -= ncl;
    
     p2[thetai]=x[thetai]-delti[thetai]/k;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    return m;
     k4=func(p2)-fx;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
 #ifdef DEBUG  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     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);     */
 #endif  }
   }  
   return res;  /*************************free matrix ************************/
 }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
 /************** Inverse of matrix **************/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 void ludcmp(double **a, int n, int *indx, double *d)    free((FREE_ARG)(m+nrl-NR_END));
 {  }
   int i,imax,j,k;  
   double big,dum,sum,temp;  /******************* ma3x *******************************/
   double *vv;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
    {
   vv=vector(1,n);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   *d=1.0;    double ***m;
   for (i=1;i<=n;i++) {  
     big=0.0;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for (j=1;j<=n;j++)    if (!m) nrerror("allocation failure 1 in matrix()");
       if ((temp=fabs(a[i][j])) > big) big=temp;    m += NR_END;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    m -= nrl;
     vv[i]=1.0/big;  
   }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   for (j=1;j<=n;j++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for (i=1;i<j;i++) {    m[nrl] += NR_END;
       sum=a[i][j];    m[nrl] -= ncl;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }  
     big=0.0;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     for (i=j;i<=n;i++) {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       sum=a[i][j];    m[nrl][ncl] += NR_END;
       for (k=1;k<j;k++)    m[nrl][ncl] -= nll;
         sum -= a[i][k]*a[k][j];    for (j=ncl+1; j<=nch; j++) 
       a[i][j]=sum;      m[nrl][j]=m[nrl][j-1]+nlay;
       if ( (dum=vv[i]*fabs(sum)) >= big) {    
         big=dum;    for (i=nrl+1; i<=nrh; i++) {
         imax=i;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       }      for (j=ncl+1; j<=nch; j++) 
     }        m[i][j]=m[i][j-1]+nlay;
     if (j != imax) {    }
       for (k=1;k<=n;k++) {    return m; 
         dum=a[imax][k];    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         a[imax][k]=a[j][k];             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         a[j][k]=dum;    */
       }  }
       *d = -(*d);  
       vv[imax]=vv[j];  /*************************free ma3x ************************/
     }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     indx[j]=imax;  {
     if (a[j][j] == 0.0) a[j][j]=TINY;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     if (j != n) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       dum=1.0/(a[j][j]);    free((FREE_ARG)(m+nrl-NR_END));
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  }
     }  
   }  /*************** function subdirf ***********/
   free_vector(vv,1,n);  /* Doesn't work */  char *subdirf(char fileres[])
 ;  {
 }    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
 void lubksb(double **a, int n, int *indx, double b[])    strcat(tmpout,"/"); /* Add to the right */
 {    strcat(tmpout,fileres);
   int i,ii=0,ip,j;    return tmpout;
   double sum;  }
    
   for (i=1;i<=n;i++) {  /*************** function subdirf2 ***********/
     ip=indx[i];  char *subdirf2(char fileres[], char *preop)
     sum=b[ip];  {
     b[ip]=b[i];    
     if (ii)    /* Caution optionfilefiname is hidden */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    strcpy(tmpout,optionfilefiname);
     else if (sum) ii=i;    strcat(tmpout,"/");
     b[i]=sum;    strcat(tmpout,preop);
   }    strcat(tmpout,fileres);
   for (i=n;i>=1;i--) {    return tmpout;
     sum=b[i];  }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];  /*************** function subdirf3 ***********/
   }  char *subdirf3(char fileres[], char *preop, char *preop2)
 }  {
     
 /************ Frequencies ********************/    /* Caution optionfilefiname is hidden */
 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)    strcpy(tmpout,optionfilefiname);
 {  /* Some frequencies */    strcat(tmpout,"/");
      strcat(tmpout,preop);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    strcat(tmpout,preop2);
   double ***freq; /* Frequencies */    strcat(tmpout,fileres);
   double *pp;    return tmpout;
   double pos, k2, dateintsum=0,k2cpt=0;  }
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];  char *asc_diff_time(long time_sec, char ascdiff[])
    {
   pp=vector(1,nlstate);    long sec_left, days, hours, minutes;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    days = (time_sec) / (60*60*24);
   strcpy(fileresp,"p");    sec_left = (time_sec) % (60*60*24);
   strcat(fileresp,fileres);    hours = (sec_left) / (60*60) ;
   if((ficresp=fopen(fileresp,"w"))==NULL) {    sec_left = (sec_left) %(60*60);
     printf("Problem with prevalence resultfile: %s\n", fileresp);    minutes = (sec_left) /60;
     exit(0);    sec_left = (sec_left) % (60);
   }    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    return ascdiff;
   j1=0;  }
    
   j=cptcoveff;  /***************** f1dim *************************/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  extern int ncom; 
    extern double *pcom,*xicom;
   for(k1=1; k1<=j;k1++){  extern double (*nrfunc)(double []); 
     for(i1=1; i1<=ncodemax[k1];i1++){   
       j1++;  double f1dim(double x) 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  { 
         scanf("%d", i);*/    int j; 
       for (i=-1; i<=nlstate+ndeath; i++)      double f;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      double *xt; 
           for(m=agemin; m <= agemax+3; m++)   
             freq[i][jk][m]=0;    xt=vector(1,ncom); 
          for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       dateintsum=0;    f=(*nrfunc)(xt); 
       k2cpt=0;    free_vector(xt,1,ncom); 
       for (i=1; i<=imx; i++) {    return f; 
         bool=1;  } 
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)  /*****************brent *************************/
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
               bool=0;  { 
         }    int iter; 
         if (bool==1) {    double a,b,d,etemp;
           for(m=firstpass; m<=lastpass; m++){    double fu=0,fv,fw,fx;
             k2=anint[m][i]+(mint[m][i]/12.);    double ftemp=0.;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;    double e=0.0; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;   
               if (m<lastpass) {    a=(ax < cx ? ax : cx); 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    b=(ax > cx ? ax : cx); 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    x=w=v=bx; 
               }    fw=fv=fx=(*f)(x); 
                  for (iter=1;iter<=ITMAX;iter++) { 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      xm=0.5*(a+b); 
                 dateintsum=dateintsum+k2;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
                 k2cpt++;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
               }      printf(".");fflush(stdout);
             }      fprintf(ficlog,".");fflush(ficlog);
           }  #ifdef DEBUGBRENT
         }      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 ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       if  (cptcovn>0) {        *xmin=x; 
         fprintf(ficresp, "\n#********** Variable ");        return fx; 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      } 
         fprintf(ficresp, "**********\n#");      ftemp=fu;
       }      if (fabs(e) > tol1) { 
       for(i=1; i<=nlstate;i++)        r=(x-w)*(fx-fv); 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        q=(x-v)*(fx-fw); 
       fprintf(ficresp, "\n");        p=(x-v)*q-(x-w)*r; 
              q=2.0*(q-r); 
       for(i=(int)agemin; i <= (int)agemax+3; i++){        if (q > 0.0) p = -p; 
         if(i==(int)agemax+3)        q=fabs(q); 
           printf("Total");        etemp=e; 
         else        e=d; 
           printf("Age %d", i);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         for(jk=1; jk <=nlstate ; jk++){          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        else { 
             pp[jk] += freq[jk][m][i];          d=p/q; 
         }          u=x+d; 
         for(jk=1; jk <=nlstate ; jk++){          if (u-a < tol2 || b-u < tol2) 
           for(m=-1, pos=0; m <=0 ; m++)            d=SIGN(tol1,xm-x); 
             pos += freq[jk][m][i];        } 
           if(pp[jk]>=1.e-10)      } else { 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           else      } 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         }      fu=(*f)(u); 
       if (fu <= fx) { 
         for(jk=1; jk <=nlstate ; jk++){        if (u >= x) a=x; else b=x; 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        SHFT(v,w,x,u) 
             pp[jk] += freq[jk][m][i];          SHFT(fv,fw,fx,fu) 
         }          } else { 
             if (u < x) a=u; else b=u; 
         for(jk=1,pos=0; jk <=nlstate ; jk++)            if (fu <= fw || w == x) { 
           pos += pp[jk];              v=w; 
         for(jk=1; jk <=nlstate ; jk++){              w=u; 
           if(pos>=1.e-5)              fv=fw; 
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              fw=fu; 
           else            } else if (fu <= fv || v == x || v == w) { 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);              v=u; 
           if( i <= (int) agemax){              fv=fu; 
             if(pos>=1.e-5){            } 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          } 
               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]);*/    nrerror("Too many iterations in brent"); 
             }    *xmin=x; 
             else    return fx; 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  } 
           }  
         }  /****************** mnbrak ***********************/
          
         for(jk=-1; jk <=nlstate+ndeath; jk++)  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
           for(m=-1; m <=nlstate+ndeath; m++)              double (*func)(double)) 
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  { 
         if(i <= (int) agemax)    double ulim,u,r,q, dum;
           fprintf(ficresp,"\n");    double fu; 
         printf("\n");   
       }    *fa=(*func)(*ax); 
     }    *fb=(*func)(*bx); 
   }    if (*fb > *fa) { 
   dateintmean=dateintsum/k2cpt;      SHFT(dum,*ax,*bx,dum) 
          SHFT(dum,*fb,*fa,dum) 
   fclose(ficresp);        } 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    *cx=(*bx)+GOLD*(*bx-*ax); 
   free_vector(pp,1,nlstate);    *fc=(*func)(*cx); 
      while (*fb > *fc) { /* Declining fa, fb, fc */
   /* End of Freq */      r=(*bx-*ax)*(*fb-*fc); 
 }      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 /************ Prevalence ********************/        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
 {  /* Some frequencies */      if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
          fu=(*func)(u); 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  #ifdef DEBUG
   double ***freq; /* Frequencies */        /* f(x)=A(x-u)**2+f(u) */
   double *pp;        double A, fparabu; 
   double pos, k2;        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
         fparabu= *fa - A*(*ax-u)*(*ax-u);
   pp=vector(1,nlstate);        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);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        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 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
   j1=0;        fu=(*func)(u); 
          if (fu < *fc) { 
   j=cptcoveff;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            SHFT(*fb,*fc,fu,(*func)(u)) 
              } 
   for(k1=1; k1<=j;k1++){      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
     for(i1=1; i1<=ncodemax[k1];i1++){        u=ulim; 
       j1++;        fu=(*func)(u); 
            } else { 
       for (i=-1; i<=nlstate+ndeath; i++)          u=(*cx)+GOLD*(*cx-*bx); 
         for (jk=-1; jk<=nlstate+ndeath; jk++)          fu=(*func)(u); 
           for(m=agemin; m <= agemax+3; m++)      } 
             freq[i][jk][m]=0;      SHFT(*ax,*bx,*cx,u) 
              SHFT(*fa,*fb,*fc,fu) 
       for (i=1; i<=imx; i++) {        } 
         bool=1;  } 
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)  /*************** linmin ************************/
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
               bool=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
         if (bool==1) {  the value of func at the returned location p . This is actually all accomplished by calling the
           for(m=firstpass; m<=lastpass; m++){  routines mnbrak and brent .*/
             k2=anint[m][i]+(mint[m][i]/12.);  int ncom; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  double *pcom,*xicom;
               if(agev[m][i]==0) agev[m][i]=agemax+1;  double (*nrfunc)(double []); 
               if(agev[m][i]==1) agev[m][i]=agemax+2;   
               if (m<lastpass) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
                 if (calagedate>0)  { 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    double brent(double ax, double bx, double cx, 
                 else                 double (*f)(double), double tol, double *xmin); 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double f1dim(double x); 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
               }                double *fc, double (*func)(double)); 
             }    int j; 
           }    double xx,xmin,bx,ax; 
         }    double fx,fb,fa;
       }   
       for(i=(int)agemin; i <= (int)agemax+3; i++){    ncom=n; 
         for(jk=1; jk <=nlstate ; jk++){    pcom=vector(1,n); 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    xicom=vector(1,n); 
             pp[jk] += freq[jk][m][i];    nrfunc=func; 
         }    for (j=1;j<=n;j++) { 
         for(jk=1; jk <=nlstate ; jk++){      pcom[j]=p[j]; 
           for(m=-1, pos=0; m <=0 ; m++)      xicom[j]=xi[j]; 
             pos += freq[jk][m][i];    } 
         }    ax=0.0; 
            xx=1.0; 
         for(jk=1; jk <=nlstate ; jk++){    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
             pp[jk] += freq[jk][m][i];  #ifdef DEBUG
         }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
            fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  #endif
            for (j=1;j<=n;j++) { 
         for(jk=1; jk <=nlstate ; jk++){          xi[j] *= xmin; 
           if( i <= (int) agemax){      p[j] += xi[j]; 
             if(pos>=1.e-5){    } 
               probs[i][jk][j1]= pp[jk]/pos;    free_vector(xicom,1,n); 
             }    free_vector(pcom,1,n); 
           }  } 
         }  
          
       }  /*************** powell ************************/
     }  /*
   }  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-
    rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  such that failure to decrease by more than this amount on one iteration signals doneness. On
   free_vector(pp,1,nlstate);  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.
 }  /* End of Freq */   */
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 /************* Waves Concatenation ***************/              double (*func)(double [])) 
   { 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    void linmin(double p[], double xi[], int n, double *fret, 
 {                double (*func)(double [])); 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    int i,ibig,j; 
      Death is a valid wave (if date is known).    double del,t,*pt,*ptt,*xit;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    double fp,fptt;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    double *xits;
      and mw[mi+1][i]. dh depends on stepm.    int niterf, itmp;
      */  
     pt=vector(1,n); 
   int i, mi, m;    ptt=vector(1,n); 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    xit=vector(1,n); 
      double sum=0., jmean=0.;*/    xits=vector(1,n); 
     *fret=(*func)(p); 
   int j, k=0,jk, ju, jl;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double sum=0.;      rcurr_time = time(NULL);  
   jmin=1e+5;    for (*iter=1;;++(*iter)) { 
   jmax=-1;      fp=(*fret); 
   jmean=0.;      ibig=0; 
   for(i=1; i<=imx; i++){      del=0.0; 
     mi=0;      rlast_time=rcurr_time;
     m=firstpass;      /* (void) gettimeofday(&curr_time,&tzp); */
     while(s[m][i] <= nlstate){      rcurr_time = time(NULL);  
       if(s[m][i]>=1)      curr_time = *localtime(&rcurr_time);
         mw[++mi][i]=m;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       if(m >=lastpass)      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
         break;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
       else     for (i=1;i<=n;i++) {
         m++;        printf(" %d %.12f",i, p[i]);
     }/* end while */        fprintf(ficlog," %d %.12lf",i, p[i]);
     if (s[m][i] > nlstate){        fprintf(ficrespow," %.12lf", p[i]);
       mi++;     /* Death is another wave */      }
       /* if(mi==0)  never been interviewed correctly before death */      printf("\n");
          /* Only death is a correct wave */      fprintf(ficlog,"\n");
       mw[mi][i]=m;      fprintf(ficrespow,"\n");fflush(ficrespow);
     }      if(*iter <=3){
         tml = *localtime(&rcurr_time);
     wav[i]=mi;        strcpy(strcurr,asctime(&tml));
     if(mi==0)        rforecast_time=rcurr_time; 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        itmp = strlen(strcurr);
   }        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           strcurr[itmp-1]='\0';
   for(i=1; i<=imx; i++){        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
     for(mi=1; mi<wav[i];mi++){        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       if (stepm <=0)        for(niterf=10;niterf<=30;niterf+=10){
         dh[mi][i]=1;          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
       else{          forecast_time = *localtime(&rforecast_time);
         if (s[mw[mi+1][i]][i] > nlstate) {          strcpy(strfor,asctime(&forecast_time));
           if (agedc[i] < 2*AGESUP) {          itmp = strlen(strfor);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          if(strfor[itmp-1]=='\n')
           if(j==0) j=1;  /* Survives at least one month after exam */          strfor[itmp-1]='\0';
           k=k+1;          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
           if (j >= jmax) jmax=j;          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);
           if (j <= jmin) jmin=j;        }
           sum=sum+j;      }
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      for (i=1;i<=n;i++) { 
           }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         }        fptt=(*fret); 
         else{  #ifdef DEBUG
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
           k=k+1;            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
           if (j >= jmax) jmax=j;  #endif
           else if (j <= jmin)jmin=j;        printf("%d",i);fflush(stdout);
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        fprintf(ficlog,"%d",i);fflush(ficlog);
           sum=sum+j;        linmin(p,xit,n,fret,func); 
         }        if (fabs(fptt-(*fret)) > del) { 
         jk= j/stepm;          del=fabs(fptt-(*fret)); 
         jl= j -jk*stepm;          ibig=i; 
         ju= j -(jk+1)*stepm;        } 
         if(jl <= -ju)  #ifdef DEBUG
           dh[mi][i]=jk;        printf("%d %.12e",i,(*fret));
         else        fprintf(ficlog,"%d %.12e",i,(*fret));
           dh[mi][i]=jk+1;        for (j=1;j<=n;j++) {
         if(dh[mi][i]==0)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           dh[mi][i]=1; /* At least one step */          printf(" x(%d)=%.12e",j,xit[j]);
       }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     }        }
   }        for(j=1;j<=n;j++) {
   jmean=sum/k;          printf(" p(%d)=%.12e",j,p[j]);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
  }        }
 /*********** Tricode ****************************/        printf("\n");
 void tricode(int *Tvar, int **nbcode, int imx)        fprintf(ficlog,"\n");
 {  #endif
   int Ndum[20],ij=1, k, j, i;      } /* end i */
   int cptcode=0;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   cptcoveff=0;  #ifdef DEBUG
          int k[2],l;
   for (k=0; k<19; k++) Ndum[k]=0;        k[0]=1;
   for (k=1; k<=7; k++) ncodemax[k]=0;        k[1]=-1;
         printf("Max: %.12e",(*func)(p));
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
     for (i=1; i<=imx; i++) {        for (j=1;j<=n;j++) {
       ij=(int)(covar[Tvar[j]][i]);          printf(" %.12e",p[j]);
       Ndum[ij]++;          fprintf(ficlog," %.12e",p[j]);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        }
       if (ij > cptcode) cptcode=ij;        printf("\n");
     }        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
     for (i=0; i<=cptcode; i++) {          for (j=1;j<=n;j++) {
       if(Ndum[i]!=0) ncodemax[j]++;            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]);
     ij=1;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for (i=1; i<=ncodemax[j]; i++) {          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       for (k=0; k<=19; k++) {        }
         if (Ndum[k] != 0) {  #endif
           nbcode[Tvar[j]][ij]=k;  
            
           ij++;        free_vector(xit,1,n); 
         }        free_vector(xits,1,n); 
         if (ij > ncodemax[j]) break;        free_vector(ptt,1,n); 
       }          free_vector(pt,1,n); 
     }        return; 
   }        } 
       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
  for (k=0; k<19; k++) Ndum[k]=0;      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
         ptt[j]=2.0*p[j]-pt[j]; 
  for (i=1; i<=ncovmodel-2; i++) {        xit[j]=p[j]-pt[j]; 
       ij=Tvar[i];        pt[j]=p[j]; 
       Ndum[ij]++;      } 
     }      fptt=(*func)(ptt); 
       if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
  ij=1;        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
  for (i=1; i<=10; i++) {        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
    if((Ndum[i]!=0) && (i<=ncovcol)){        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
      Tvaraff[ij]=i;        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
      ij++;        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
    }        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
  }        /* Thus we compare delta(2h) with observed f1-f3 */
          /* or best gain on one ancient line 'del' with total  */
     cptcoveff=ij-1;        /* gain f1-f2 = f1 - f2 - 'del' with del  */
 }        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   
 /*********** Health Expectancies ****************/        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
         t= t- del*SQR(fp-fptt);
 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 )        printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
         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);
 {  #ifdef DEBUG
   /* Health expectancies */        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   double age, agelim, hf;        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   double ***p3mat,***varhe;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   double **dnewm,**doldm;        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
   double *xp;        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
   double **gp, **gm;  #endif
   double ***gradg, ***trgradg;        if (t < 0.0) { /* Then we use it for last direction */
   int theta;          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
           for (j=1;j<=n;j++) { 
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);            xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
   xp=vector(1,npar);            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
   dnewm=matrix(1,nlstate*2,1,npar);          }
   doldm=matrix(1,nlstate*2,1,nlstate*2);          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
            fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   fprintf(ficreseij,"# Health expectancies\n");  
   fprintf(ficreseij,"# Age");  #ifdef DEBUG
   for(i=1; i<=nlstate;i++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for(j=1; j<=nlstate;j++)          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          for(j=1;j<=n;j++){
   fprintf(ficreseij,"\n");            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
   if(estepm < stepm){          }
     printf ("Problem %d lower than %d\n",estepm, stepm);          printf("\n");
   }          fprintf(ficlog,"\n");
   else  hstepm=estepm;    #endif
   /* We compute the life expectancy from trapezoids spaced every estepm months        } /* end of t negative */
    * This is mainly to measure the difference between two models: for example      } /* end if (fptt < fp)  */
    * if stepm=24 months pijx are given only every 2 years and by summing them    } 
    * we are calculating an estimate of the Life Expectancy assuming a linear  } 
    * progression inbetween and thus overestimating or underestimating according  
    * to the curvature of the survival function. If, for the same date, we  /**** Prevalence limit (stable or period prevalence)  ****************/
    * 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  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
    * hypothesis. A more precise result, taking into account a more precise  {
    * curvature will be obtained if estepm is as small as stepm. */    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
   /* 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.    int i, ii,j,k;
      nhstepm is the number of hstepm from age to agelim    double min, max, maxmin, maxmax,sumnew=0.;
      nstepm is the number of stepm from age to agelin.    /* double **matprod2(); */ /* test */
      Look at hpijx to understand the reason of that which relies in memory size    double **out, cov[NCOVMAX+1], **pmij();
      and note for a fixed period like estepm months */    double **newm;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    double agefin, delaymax=50 ; /* Max number of years to converge */
      survival function given by stepm (the optimization length). Unfortunately it    
      means that if the survival funtion is printed only each two years of age and if    for (ii=1;ii<=nlstate+ndeath;ii++)
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      for (j=1;j<=nlstate+ndeath;j++){
      results. So we changed our mind and took the option of the best precision.        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   */      }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    
     cov[1]=1.;
   agelim=AGESUP;    
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     /* nhstepm age range expressed in number of stepm */    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      newm=savm;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */      /* Covariates have to be included here again */
     /* if (stepm >= YEARM) hstepm=1;*/      cov[2]=agefin;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (k=1; k<=cptcovn;k++) {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     gp=matrix(0,nhstepm,1,nlstate*2);        /*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]]);*/
     gm=matrix(0,nhstepm,1,nlstate*2);      }
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        
        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     /* Computing Variances of health expectancies */      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
      for(theta=1; theta <=npar; theta++){      
       for(i=1; i<=npar; i++){      savm=oldm;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      oldm=newm;
       }      maxmax=0.;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for(j=1;j<=nlstate;j++){
          min=1.;
       cptj=0;        max=0.;
       for(j=1; j<= nlstate; j++){        for(i=1; i<=nlstate; i++) {
         for(i=1; i<=nlstate; i++){          sumnew=0;
           cptj=cptj+1;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){          prlim[i][j]= newm[i][j]/(1-sumnew);
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
           }          max=FMAX(max,prlim[i][j]);
         }          min=FMIN(min,prlim[i][j]);
       }        }
              maxmin=max-min;
              maxmax=FMAX(maxmax,maxmin);
       for(i=1; i<=npar; i++)      } /* j loop */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      if(maxmax < ftolpl){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          return prlim;
            }
       cptj=0;    } /* age loop */
       for(j=1; j<= nlstate; j++){    return prlim; /* should not reach here */
         for(i=1;i<=nlstate;i++){  }
           cptj=cptj+1;  
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){  /*************** transition probabilities ***************/ 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         }  {
       }    /* According to parameters values stored in x and the covariate's values stored in cov,
       for(j=1; j<= nlstate*2; j++)       computes the probability to be observed in state j being in state i by appying the
         for(h=0; h<=nhstepm-1; h++){       model to the ncovmodel covariates (including constant and age).
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];       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
 /* End theta */       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
        Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);       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
      for(h=0; h<=nhstepm-1; h++)       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
       for(j=1; j<=nlstate*2;j++)    */
         for(theta=1; theta <=npar; theta++)    double s1, lnpijopii;
           trgradg[h][j][theta]=gradg[h][theta][j];    /*double t34;*/
          int i,j, nc, ii, jj;
   
      for(i=1;i<=nlstate*2;i++)      for(i=1; i<= nlstate; i++){
       for(j=1;j<=nlstate*2;j++)        for(j=1; j<i;j++){
         varhe[i][j][(int)age] =0.;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
             /*lnpijopii += param[i][j][nc]*cov[nc];*/
      printf("%d|",(int)age);fflush(stdout);            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
      for(h=0;h<=nhstepm-1;h++){  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       for(k=0;k<=nhstepm-1;k++){          }
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         for(i=1;i<=nlstate*2;i++)        }
           for(j=1;j<=nlstate*2;j++)        for(j=i+1; j<=nlstate+ndeath;j++){
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       }            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     }            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
                }
     /* Computing expectancies */          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     for(i=1; i<=nlstate;i++)        }
       for(j=1; j<=nlstate;j++)      }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      for(i=1; i<= nlstate; i++){
                  s1=0;
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/        for(j=1; j<i; j++){
           s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         }          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }
     fprintf(ficreseij,"%3.0f",age );        for(j=i+1; j<=nlstate+ndeath; j++){
     cptj=0;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     for(i=1; i<=nlstate;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;j++){        }
         cptj++;        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        ps[i][i]=1./(s1+1.);
       }        /* Computing other pijs */
     fprintf(ficreseij,"\n");        for(j=1; j<i; j++)
              ps[i][j]= exp(ps[i][j])*ps[i][i];
     free_matrix(gm,0,nhstepm,1,nlstate*2);        for(j=i+1; j<=nlstate+ndeath; j++)
     free_matrix(gp,0,nhstepm,1,nlstate*2);          ps[i][j]= exp(ps[i][j])*ps[i][i];
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      } /* end i */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      
   }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   free_vector(xp,1,npar);        for(jj=1; jj<= nlstate+ndeath; jj++){
   free_matrix(dnewm,1,nlstate*2,1,npar);          ps[ii][jj]=0;
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);          ps[ii][ii]=1;
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);        }
 }      }
       
 /************ Variance ******************/      
 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)      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
 {      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   /* Variance of health expectancies */      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      /*   } */
   double **newm;      /*   printf("\n "); */
   double **dnewm,**doldm;      /* } */
   int i, j, nhstepm, hstepm, h, nstepm ;      /* printf("\n ");printf("%lf ",cov[2]);*/
   int k, cptcode;      /*
   double *xp;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   double **gp, **gm;        goto end;*/
   double ***gradg, ***trgradg;      return ps;
   double ***p3mat;  }
   double age,agelim, hf;  
   int theta;  /**************** Product of 2 matrices ******************/
   
   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");  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   fprintf(ficresvij,"# Age");  {
   for(i=1; i<=nlstate;i++)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     for(j=1; j<=nlstate;j++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    /* in, b, out are matrice of pointers which should have been initialized 
   fprintf(ficresvij,"\n");       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
   xp=vector(1,npar);    int i, j, k;
   dnewm=matrix(1,nlstate,1,npar);    for(i=nrl; i<= nrh; i++)
   doldm=matrix(1,nlstate,1,nlstate);      for(k=ncolol; k<=ncoloh; k++){
          out[i][k]=0.;
   if(estepm < stepm){        for(j=ncl; j<=nch; j++)
     printf ("Problem %d lower than %d\n",estepm, stepm);          out[i][k] +=in[i][j]*b[j][k];
   }      }
   else  hstepm=estepm;      return out;
   /* For example we decided to compute the life expectancy with the smallest unit */  }
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.  
      nhstepm is the number of hstepm from age to agelim  
      nstepm is the number of stepm from age to agelin.  /************* Higher Matrix Product ***************/
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like k years */  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   /* 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    /* Computes the transition matrix starting at age 'age' over 
      means that if the survival funtion is printed only each two years of age and if       'nhstepm*hstepm*stepm' months (i.e. until
      you sum them up and add 1 year (area under the trapezoids) you won't get the same       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
      results. So we changed our mind and took the option of the best precision.       nhstepm*hstepm matrices. 
   */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */       (typically every 2 years instead of every month which is too big 
   agelim = AGESUP;       for the memory).
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       Model is determined by parameters x and covariates have to be 
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       included manually here. 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  
     gp=matrix(0,nhstepm,1,nlstate);    int i, j, d, h, k;
     gm=matrix(0,nhstepm,1,nlstate);    double **out, cov[NCOVMAX+1];
     double **newm;
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */    /* Hstepm could be zero and should return the unit matrix */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for (i=1;i<=nlstate+ndeath;i++)
       }      for (j=1;j<=nlstate+ndeath;j++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          oldm[i][j]=(i==j ? 1.0 : 0.0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
       if (popbased==1) {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         for(i=1; i<=nlstate;i++)    for(h=1; h <=nhstepm; h++){
           prlim[i][i]=probs[(int)age][i][ij];      for(d=1; d <=hstepm; d++){
       }        newm=savm;
          /* Covariates have to be included here again */
       for(j=1; j<= nlstate; j++){        cov[1]=1.;
         for(h=0; h<=nhstepm; h++){        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          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];
            for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
       for(i=1; i<=npar; i++) /* Computes gradient */          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
          /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       if (popbased==1) {        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         for(i=1; i<=nlstate;i++)                     pmij(pmmij,cov,ncovmodel,x,nlstate));
           prlim[i][i]=probs[(int)age][i][ij];        savm=oldm;
       }        oldm=newm;
       }
       for(j=1; j<= nlstate; j++){      for(i=1; i<=nlstate+ndeath; i++)
         for(h=0; h<=nhstepm; h++){        for(j=1;j<=nlstate+ndeath;j++) {
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          po[i][j][h]=newm[i][j];
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         }        }
       }      /*printf("h=%d ",h);*/
     } /* end h */
       for(j=1; j<= nlstate; j++)  /*     printf("\n H=%d \n",h); */
         for(h=0; h<=nhstepm; h++){    return po;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  }
         }  
     } /* End theta */  #ifdef NLOPT
     double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    double fret;
     double *xt;
     for(h=0; h<=nhstepm; h++)    int j;
       for(j=1; j<=nlstate;j++)    myfunc_data *d2 = (myfunc_data *) pd;
         for(theta=1; theta <=npar; theta++)  /* xt = (p1-1); */
           trgradg[h][j][theta]=gradg[h][theta][j];    xt=vector(1,n); 
     for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  
     for(i=1;i<=nlstate;i++)    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
       for(j=1;j<=nlstate;j++)    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
         vareij[i][j][(int)age] =0.;    printf("Function = %.12lf ",fret);
     for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     for(h=0;h<=nhstepm;h++){    printf("\n");
       for(k=0;k<=nhstepm;k++){   free_vector(xt,1,n);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    return fret;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  }
         for(i=1;i<=nlstate;i++)  #endif
           for(j=1;j<=nlstate;j++)  
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;  /*************** log-likelihood *************/
       }  double func( double *x)
     }  {
     int i, ii, j, k, mi, d, kk;
     fprintf(ficresvij,"%.0f ",age );    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     for(i=1; i<=nlstate;i++)    double **out;
       for(j=1; j<=nlstate;j++){    double sw; /* Sum of weights */
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    double lli; /* Individual log likelihood */
       }    int s1, s2;
     fprintf(ficresvij,"\n");    double bbh, survp;
     free_matrix(gp,0,nhstepm,1,nlstate);    long ipmx;
     free_matrix(gm,0,nhstepm,1,nlstate);    /*extern weight */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    /* We are differentiating ll according to initial status */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*for(i=1;i<imx;i++) 
   } /* End age */      printf(" %d\n",s[4][i]);
      */
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);    ++countcallfunc;
   free_matrix(dnewm,1,nlstate,1,nlstate);  
     cov[1]=1.;
 }  
     for(k=1; k<=nlstate; k++) ll[k]=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)    if(mle==1){
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* Variance of prevalence limit */        /* Computes the values of the ncovmodel covariates of the model
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
   double **newm;           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
   double **dnewm,**doldm;           to be observed in j being in i according to the model.
   int i, j, nhstepm, hstepm;         */
   int k, cptcode;        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
   double *xp;          cov[2+k]=covar[Tvar[k]][i];
   double *gp, *gm;        }
   double **gradg, **trgradg;        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
   double age,agelim;           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
   int theta;           has been calculated etc */
            for(mi=1; mi<= wav[i]-1; mi++){
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
   fprintf(ficresvpl,"# Age");            for (j=1;j<=nlstate+ndeath;j++){
   for(i=1; i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresvpl," %1d-%1d",i,i);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficresvpl,"\n");            }
           for(d=0; d<dh[mi][i]; d++){
   xp=vector(1,npar);            newm=savm;
   dnewm=matrix(1,nlstate,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   doldm=matrix(1,nlstate,1,nlstate);            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
   hstepm=1*YEARM; /* Every year of age */            }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   agelim = AGESUP;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            savm=oldm;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            oldm=newm;
     if (stepm >= YEARM) hstepm=1;          } /* end mult */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        
     gradg=matrix(1,npar,1,nlstate);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     gp=vector(1,nlstate);          /* But now since version 0.9 we anticipate for bias at large stepm.
     gm=vector(1,nlstate);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
     for(theta=1; theta <=npar; theta++){           * the nearest (and in case of equal distance, to the lowest) interval but now
       for(i=1; i<=npar; i++){ /* Computes gradient */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         xp[i] = x[i] + (i==theta ?delti[theta]:0);           * (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
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       for(i=1;i<=nlstate;i++)           * -stepm/2 to stepm/2 .
         gp[i] = prlim[i][i];           * 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. 
       for(i=1; i<=npar; i++) /* Computes gradient */           */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          s1=s[mw[mi][i]][i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          s2=s[mw[mi+1][i]][i];
       for(i=1;i<=nlstate;i++)          bbh=(double)bh[mi][i]/(double)stepm; 
         gm[i] = prlim[i][i];          /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
       for(i=1;i<=nlstate;i++)           */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     } /* End theta */          if( s2 > nlstate){ 
             /* i.e. if s2 is a death state and if the date of death is known 
     trgradg =matrix(1,nlstate,1,npar);               then the contribution to the likelihood is the probability to 
                die between last step unit time and current  step unit time, 
     for(j=1; j<=nlstate;j++)               which is also equal to probability to die before dh 
       for(theta=1; theta <=npar; theta++)               minus probability to die before dh-stepm . 
         trgradg[j][theta]=gradg[theta][j];               In version up to 0.92 likelihood was computed
           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
       varpl[i][(int)age] =0.;          and not the date of a change in health state. The former idea was
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          to consider that at each interview the state was recorded
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          (healthy, disable or death) and IMaCh was corrected; but when we
     for(i=1;i<=nlstate;i++)          introduced the exact date of death then we should have modified
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          the contribution of an exact death to the likelihood. This new
           contribution is smaller and very dependent of the step unit
     fprintf(ficresvpl,"%.0f ",age );          stepm. It is no more the probability to die between last interview
     for(i=1; i<=nlstate;i++)          and month of death but the probability to survive from last
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          interview up to one month before death multiplied by the
     fprintf(ficresvpl,"\n");          probability to die within a month. Thanks to Chris
     free_vector(gp,1,nlstate);          Jackson for correcting this bug.  Former versions increased
     free_vector(gm,1,nlstate);          mortality artificially. The bad side is that we add another loop
     free_matrix(gradg,1,npar,1,nlstate);          which slows down the processing. The difference can be up to 10%
     free_matrix(trgradg,1,nlstate,1,npar);          lower mortality.
   } /* End age */            */
             lli=log(out[s1][s2] - savm[s1][s2]);
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);          } else if  (s2==-2) {
             for (j=1,survp=0. ; j<=nlstate; j++) 
 }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             /*survp += out[s1][j]; */
 /************ Variance of one-step probabilities  ******************/            lli= log(survp);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          }
 {          
   int i, j, i1, k1, j1, z1;          else if  (s2==-4) { 
   int k=0,l, cptcode;            for (j=3,survp=0. ; j<=nlstate; j++)  
   double **dnewm,**doldm;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double *xp;            lli= log(survp); 
   double *gp, *gm;          } 
   double **gradg, **trgradg;  
   double age,agelim, cov[NCOVMAX];          else if  (s2==-5) { 
   int theta;            for (j=1,survp=0. ; j<=2; j++)  
   char fileresprob[FILENAMELENGTH];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   char fileresprobcov[FILENAMELENGTH];            lli= log(survp); 
   char fileresprobcor[FILENAMELENGTH];          } 
           
   strcpy(fileresprob,"prob");          else{
   strcat(fileresprob,fileres);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
     printf("Problem with resultfile: %s\n", fileresprob);          } 
   }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   strcpy(fileresprobcov,"probcov");          /*if(lli ==000.0)*/
   strcat(fileresprobcov,fileres);          /*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); */
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {          ipmx +=1;
     printf("Problem with resultfile: %s\n", fileresprobcov);          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   strcpy(fileresprobcor,"probcor");        } /* end of wave */
   strcat(fileresprobcor,fileres);      } /* end of individual */
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    }  else if(mle==2){
     printf("Problem with resultfile: %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];
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);        for(mi=1; mi<= wav[i]-1; mi++){
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);          for (ii=1;ii<=nlstate+ndeath;ii++)
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficresprob,"# Age");            }
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");          for(d=0; d<=dh[mi][i]; d++){
   fprintf(ficresprobcov,"# Age");            newm=savm;
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficresprobcov,"# Age");            for (kk=1; kk<=cptcovage;kk++) {
   for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(j=1; j<=(nlstate+ndeath);j++){            }
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       fprintf(ficresprobcov," p%1d-%1d ",i,j);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       fprintf(ficresprobcor," p%1d-%1d ",i,j);            savm=oldm;
     }              oldm=newm;
   fprintf(ficresprob,"\n");          } /* end mult */
   fprintf(ficresprobcov,"\n");        
   fprintf(ficresprobcor,"\n");          s1=s[mw[mi][i]][i];
   xp=vector(1,npar);          s2=s[mw[mi+1][i]][i];
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          bbh=(double)bh[mi][i]/(double)stepm; 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
            ipmx +=1;
   cov[1]=1;          sw += weight[i];
   j=cptcoveff;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        } /* end of wave */
   j1=0;      } /* end of individual */
   for(k1=1; k1<=1;k1++){    }  else if(mle==3){  /* exponential inter-extrapolation */
     for(i1=1; i1<=ncodemax[k1];i1++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     j1++;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
     if  (cptcovn>0) {          for (ii=1;ii<=nlstate+ndeath;ii++)
       fprintf(ficresprob, "\n#********** Variable ");            for (j=1;j<=nlstate+ndeath;j++){
       fprintf(ficresprobcov, "\n#********** Variable ");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresprobcor, "\n#********** Variable ");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            }
       fprintf(ficresprob, "**********\n#");          for(d=0; d<dh[mi][i]; d++){
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            newm=savm;
       fprintf(ficresprobcov, "**********\n#");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficresprobcor, "**********\n#");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }            }
                out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (age=bage; age<=fage; age ++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         cov[2]=age;            savm=oldm;
         for (k=1; k<=cptcovn;k++) {            oldm=newm;
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];          } /* end mult */
         }        
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          s1=s[mw[mi][i]][i];
         for (k=1; k<=cptcovprod;k++)          s2=s[mw[mi+1][i]][i];
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          bbh=(double)bh[mi][i]/(double)stepm; 
                  lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         gradg=matrix(1,npar,1,9);          ipmx +=1;
         trgradg=matrix(1,9,1,npar);          sw += weight[i];
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        } /* end of wave */
          } /* end of individual */
         for(theta=1; theta <=npar; theta++){    }else if (mle==4){  /* ml=4 no inter-extrapolation */
           for(i=1; i<=npar; i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             xp[i] = x[i] + (i==theta ?delti[theta]:0);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                  for(mi=1; mi<= wav[i]-1; mi++){
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
                      for (j=1;j<=nlstate+ndeath;j++){
           k=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(i=1; i<= (nlstate+ndeath); i++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             for(j=1; j<=(nlstate+ndeath);j++){            }
               k=k+1;          for(d=0; d<dh[mi][i]; d++){
               gp[k]=pmmij[i][j];            newm=savm;
             }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           }            for (kk=1; kk<=cptcovage;kk++) {
                        cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           for(i=1; i<=npar; i++)            }
             xp[i] = x[i] - (i==theta ?delti[theta]:0);          
                out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           k=0;            savm=oldm;
           for(i=1; i<=(nlstate+ndeath); i++){            oldm=newm;
             for(j=1; j<=(nlstate+ndeath);j++){          } /* end mult */
               k=k+1;        
               gm[k]=pmmij[i][j];          s1=s[mw[mi][i]][i];
             }          s2=s[mw[mi+1][i]][i];
           }          if( s2 > nlstate){ 
                  lli=log(out[s1][s2] - savm[s1][s2]);
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          }else{
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         }          }
           ipmx +=1;
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          sw += weight[i];
           for(theta=1; theta <=npar; theta++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             trgradg[j][theta]=gradg[theta][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 */
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      } /* end of individual */
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
              for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         pmij(pmmij,cov,ncovmodel,x,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                for(mi=1; mi<= wav[i]-1; mi++){
         k=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
         for(i=1; i<=(nlstate+ndeath); i++){            for (j=1;j<=nlstate+ndeath;j++){
           for(j=1; j<=(nlstate+ndeath);j++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             k=k+1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             gm[k]=pmmij[i][j];            }
           }          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
                  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         /*printf("\n%d ",(int)age);            for (kk=1; kk<=cptcovage;kk++) {
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            }
      }*/          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         fprintf(ficresprob,"\n%d ",(int)age);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         fprintf(ficresprobcov,"\n%d ",(int)age);            savm=oldm;
         fprintf(ficresprobcor,"\n%d ",(int)age);            oldm=newm;
           } /* end mult */
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)        
           fprintf(ficresprob,"%12.3e (%12.3e) ",gm[i],sqrt(doldm[i][j]));          s1=s[mw[mi][i]][i];
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){          s2=s[mw[mi+1][i]][i];
           fprintf(ficresprobcov,"%12.3e ",gm[i]);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           fprintf(ficresprobcor,"%12.3e ",gm[i]);          ipmx +=1;
         }          sw += weight[i];
         i=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for (k=1; k<=(nlstate);k++){          /*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 (l=1; l<=(nlstate+ndeath);l++){        } /* end of wave */
             i=i++;      } /* end of individual */
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    } /* End of if */
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
             for (j=1; j<=i;j++){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
               fprintf(ficresprobcov," %12.3e",doldm[i][j]);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
               fprintf(ficresprobcor," %12.3e",doldm[i][j]/sqrt(doldm[i][i])/sqrt(doldm[j][j]));    return -l;
             }  }
           }  
         }  /*************** log-likelihood *************/
       }  double funcone( double *x)
     }  {
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    /* Same as likeli but slower because of a lot of printf and if */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    int i, ii, j, k, mi, d, kk;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double **out;
   }    double lli; /* Individual log likelihood */
   free_vector(xp,1,npar);    double llt;
   fclose(ficresprob);    int s1, s2;
   fclose(ficresprobcov);    double bbh, survp;
   fclose(ficresprobcor);    /*extern weight */
 }    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
 /******************* Printing html file ***********/      printf(" %d\n",s[4][i]);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    */
                   int lastpass, int stepm, int weightopt, char model[],\    cov[1]=1.;
                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \  
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\    for(k=1; k<=nlstate; k++) ll[k]=0.;
                   char version[], int popforecast, int estepm ,\  
                   double jprev1, double mprev1,double anprev1, \    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   double jprev2, double mprev2,double anprev2){      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int jj1, k1, i1, cpt;      for(mi=1; mi<= wav[i]-1; mi++){
   FILE *fichtm;        for (ii=1;ii<=nlstate+ndeath;ii++)
   /*char optionfilehtm[FILENAMELENGTH];*/          for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcpy(optionfilehtm,optionfile);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcat(optionfilehtm,".htm");          }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        for(d=0; d<dh[mi][i]; d++){
     printf("Problem with %s \n",optionfilehtm), exit(0);          newm=savm;
   }          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n          }
 \n          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
 Total number of observations=%d <br>\n          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 <hr  size=\"2\" color=\"#EC5E5E\">          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
  <ul><li>Parameter files<br>\n          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n          savm=oldm;
  - 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);          oldm=newm;
         } /* end mult */
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n        
  - 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        s1=s[mw[mi][i]][i];
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n        s2=s[mw[mi+1][i]][i];
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n        bbh=(double)bh[mi][i]/(double)stepm; 
  - Life expectancies by age and initial health status (estepm=%2d months):        /* bias is positive if real duration
    <a href=\"e%s\">e%s</a> <br>\n</li>", \         * is higher than the multiple of stepm and negative otherwise.
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);         */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n          lli=log(out[s1][s2] - savm[s1][s2]);
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n        } else if  (s2==-2) {
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n          for (j=1,survp=0. ; j<=nlstate; j++) 
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n          lli= log(survp);
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n        }else if (mle==1){
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
  - 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);        } else if(mle==2){
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
  if(popforecast==1) fprintf(fichtm,"\n        } else if(mle==3){  /* exponential inter-extrapolation */
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         <br>",fileres,fileres,fileres,fileres);          lli=log(out[s1][s2]); /* Original formula */
  else        } else{  /* mle=0 back to 1 */
    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);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 fprintf(fichtm," <li>Graphs</li><p>");          /*lli=log(out[s1][s2]); */ /* Original formula */
         } /* End of if */
  m=cptcoveff;        ipmx +=1;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
  jj1=0;        /*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(k1=1; k1<=m;k1++){        if(globpr){
    for(i1=1; i1<=ncodemax[k1];i1++){          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
      jj1++;   %11.6f %11.6f %11.6f ", \
      if (cptcovn > 0) {                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
        for (cpt=1; cpt<=cptcoveff;cpt++)          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            llt +=ll[k]*gipmx/gsw;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
      }          }
      /* Pij */          fprintf(ficresilk," %10.6f\n", -llt);
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>        }
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          } /* end of wave */
      /* Quasi-incidences */    } /* end of individual */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
        /* Stable prevalence in each health state */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
        for(cpt=1; cpt<nlstate;cpt++){    if(globpr==0){ /* First time we count the contributions and weights */
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>      gipmx=ipmx;
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      gsw=sw;
        }    }
     for(cpt=1; cpt<=nlstate;cpt++) {    return -l;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  }
 interval) in state (%d): v%s%d%d.png <br>  
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
      }  /*************** function likelione ***********/
      for(cpt=1; cpt<=nlstate;cpt++) {  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>  {
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    /* This routine should help understanding what is done with 
      }       the selection of individuals/waves and
      fprintf(fichtm,"\n<br>- Total life expectancy by age and       to check the exact contribution to the likelihood.
 health expectancies in states (1) and (2): e%s%d.png<br>       Plotting could be done.
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     */
 fprintf(fichtm,"\n</body>");    int k;
    }  
  }    if(*globpri !=0){ /* Just counts and sums, no printings */
 fclose(fichtm);      strcpy(fileresilk,"ilk"); 
 }      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
 /******************* Gnuplot file **************/        printf("Problem with resultfile: %s\n", fileresilk);
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      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");
   int ng;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   strcpy(optionfilegnuplot,optionfilefiname);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   strcat(optionfilegnuplot,".gp");      for(k=1; k<=nlstate; k++) 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     printf("Problem with file %s",optionfilegnuplot);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   }    }
   
 #ifdef windows    *fretone=(*funcone)(p);
     fprintf(ficgp,"cd \"%s\" \n",pathc);    if(*globpri !=0){
 #endif      fclose(ficresilk);
 m=pow(2,cptcoveff);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
        fflush(fichtm); 
  /* 1eme*/    } 
   for (cpt=1; cpt<= nlstate ; cpt ++) {    return;
    for (k1=1; k1<= m ; k1 ++) {  }
   
 #ifdef windows  
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  /*********** Maximum Likelihood Estimation ***************/
      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  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 #ifdef unix  {
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    int i,j, iter=0;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    double **xi;
 #endif    double fret;
     double fretone; /* Only one call to likelihood */
 for (i=1; i<= nlstate ; i ++) {    /*  char filerespow[FILENAMELENGTH];*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  #ifdef NLOPT
 }    int creturn;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    nlopt_opt opt;
     for (i=1; i<= nlstate ; i ++) {    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double *lb;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double minf; /* the minimum objective value, upon return */
 }    double * p1; /* Shifted parameters from 0 instead of 1 */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    myfunc_data dinst, *d = &dinst;
      for (i=1; i<= nlstate ; i ++) {  #endif
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      xi=matrix(1,npar,1,npar);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    for (i=1;i<=npar;i++)
 #ifdef unix      for (j=1;j<=npar;j++)
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");        xi[i][j]=(i==j ? 1.0 : 0.0);
 #endif    printf("Powell\n");  fprintf(ficlog,"Powell\n");
    }    strcpy(filerespow,"pow"); 
   }    strcat(filerespow,fileres);
   /*2 eme*/    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
   for (k1=1; k1<= m ; k1 ++) {      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);    }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
        for (i=1;i<=nlstate;i++)
     for (i=1; i<= nlstate+1 ; i ++) {      for(j=1;j<=nlstate+ndeath;j++)
       k=2*i;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficrespow,"\n");
       for (j=1; j<= nlstate+1 ; j ++) {  #ifdef POWELL
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    powell(p,xi,npar,ftol,&iter,&fret,func);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  #endif
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  #ifdef NLOPT
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  #ifdef NEWUOA
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
       for (j=1; j<= nlstate+1 ; j ++) {  #else
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
         else fprintf(ficgp," \%%*lf (\%%*lf)");  #endif
 }      lb=vector(0,npar-1);
       fprintf(ficgp,"\" t\"\" w l 0,");    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    nlopt_set_lower_bounds(opt, lb);
       for (j=1; j<= nlstate+1 ; j ++) {    nlopt_set_initial_step1(opt, 0.1);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
 }      d->function = func;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
       else fprintf(ficgp,"\" t\"\" w l 0,");    nlopt_set_min_objective(opt, myfunc, d);
     }    nlopt_set_xtol_rel(opt, ftol);
   }    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
        printf("nlopt failed! %d\n",creturn); 
   /*3eme*/    }
     else {
   for (k1=1; k1<= m ; k1 ++) {      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
     for (cpt=1; cpt<= nlstate ; cpt ++) {      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       k=2+nlstate*(2*cpt-2);      iter=1; /* not equal */
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    }
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    nlopt_destroy(opt);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  #endif
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    free_matrix(xi,1,npar,1,npar);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    fclose(ficrespow);
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   
 */  }
       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);  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       }  {
     }    double  **a,**y,*x,pd;
   }    double **hess;
      int i, j;
   /* CV preval stat */    int *indx;
     for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       k=3;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    void lubksb(double **a, int npar, int *indx, double b[]) ;
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
       for (i=1; i< nlstate ; i ++)    hess=matrix(1,npar,1,npar);
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    printf("\nCalculation of the hessian matrix. Wait...\n");
          fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       l=3+(nlstate+ndeath)*cpt;    for (i=1;i<=npar;i++){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      printf("%d",i);fflush(stdout);
       for (i=1; i< nlstate ; i ++) {      fprintf(ficlog,"%d",i);fflush(ficlog);
         l=3+(nlstate+ndeath)*cpt;     
         fprintf(ficgp,"+$%d",l+i+1);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       }      
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        /*  printf(" %f ",p[i]);
     }          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   }      }
      
   /* proba elementaires */    for (i=1;i<=npar;i++) {
    for(i=1,jk=1; i <=nlstate; i++){      for (j=1;j<=npar;j++)  {
     for(k=1; k <=(nlstate+ndeath); k++){        if (j>i) { 
       if (k != i) {          printf(".%d%d",i,j);fflush(stdout);
         for(j=1; j <=ncovmodel; j++){          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                  hess[i][j]=hessij(p,delti,i,j,func,npar);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          
           jk++;          hess[j][i]=hess[i][j];    
           fprintf(ficgp,"\n");          /*printf(" %lf ",hess[i][j]);*/
         }        }
       }      }
     }    }
    }    printf("\n");
     fprintf(ficlog,"\n");
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/  
      for(jk=1; jk <=m; jk++) {    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
        if (ng==2)    
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    a=matrix(1,npar,1,npar);
        else    y=matrix(1,npar,1,npar);
          fprintf(ficgp,"\nset title \"Probability\"\n");    x=vector(1,npar);
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    indx=ivector(1,npar);
        i=1;    for (i=1;i<=npar;i++)
        for(k2=1; k2<=nlstate; k2++) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
          k3=i;    ludcmp(a,npar,indx,&pd);
          for(k=1; k<=(nlstate+ndeath); k++) {  
            if (k != k2){    for (j=1;j<=npar;j++) {
              if(ng==2)      for (i=1;i<=npar;i++) x[i]=0;
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);      x[j]=1;
              else      lubksb(a,npar,indx,x);
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      for (i=1;i<=npar;i++){ 
              ij=1;        matcov[i][j]=x[i];
              for(j=3; j <=ncovmodel; j++) {      }
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    }
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
                  ij++;    printf("\n#Hessian matrix#\n");
                }    fprintf(ficlog,"\n#Hessian matrix#\n");
                else    for (i=1;i<=npar;i++) { 
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      for (j=1;j<=npar;j++) { 
              }        printf("%.3e ",hess[i][j]);
              fprintf(ficgp,")/(1");        fprintf(ficlog,"%.3e ",hess[i][j]);
                    }
              for(k1=1; k1 <=nlstate; k1++){        printf("\n");
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      fprintf(ficlog,"\n");
                ij=1;    }
                for(j=3; j <=ncovmodel; j++){  
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /* Recompute Inverse */
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    for (i=1;i<=npar;i++)
                    ij++;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
                  }    ludcmp(a,npar,indx,&pd);
                  else  
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /*  printf("\n#Hessian matrix recomputed#\n");
                }  
                fprintf(ficgp,")");    for (j=1;j<=npar;j++) {
              }      for (i=1;i<=npar;i++) x[i]=0;
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);      x[j]=1;
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      lubksb(a,npar,indx,x);
              i=i+ncovmodel;      for (i=1;i<=npar;i++){ 
            }        y[i][j]=x[i];
          }        printf("%.3e ",y[i][j]);
        }        fprintf(ficlog,"%.3e ",y[i][j]);
      }      }
    }      printf("\n");
    fclose(ficgp);      fprintf(ficlog,"\n");
 }  /* end gnuplot */    }
     */
   
 /*************** Moving average **************/    free_matrix(a,1,npar,1,npar);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
   int i, cpt, cptcod;    free_ivector(indx,1,npar);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    free_matrix(hess,1,npar,1,npar);
       for (i=1; i<=nlstate;i++)  
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  
           mobaverage[(int)agedeb][i][cptcod]=0.;  }
      
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){  /*************** hessian matrix ****************/
       for (i=1; i<=nlstate;i++){  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  {
           for (cpt=0;cpt<=4;cpt++){    int i;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    int l=1, lmax=20;
           }    double k1,k2;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    double p2[MAXPARM+1]; /* identical to x */
         }    double res;
       }    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     }    double fx;
        int k=0,kmax=10;
 }    double l1;
   
     fx=func(x);
 /************** Forecasting ******************/    for (i=1;i<=npar;i++) p2[i]=x[i];
 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){    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
        l1=pow(10,l);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      delts=delt;
   int *popage;      for(k=1 ; k <kmax; k=k+1){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        delt = delta*(l1*k);
   double *popeffectif,*popcount;        p2[theta]=x[theta] +delt;
   double ***p3mat;        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
   char fileresf[FILENAMELENGTH];        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
  agelim=AGESUP;        /*res= (k1-2.0*fx+k2)/delt/delt; */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  #ifdef DEBUGHESS
          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);
   strcpy(fileresf,"f");  #endif
   strcat(fileresf,fileres);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   if((ficresf=fopen(fileresf,"w"))==NULL) {        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     printf("Problem with forecast resultfile: %s\n", fileresf);          k=kmax;
   }        }
   printf("Computing forecasting: result on file '%s' \n", fileresf);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   if (mobilav==1) {          delts=delt;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
     movingaverage(agedeb, fage, ageminpar, mobaverage);      }
   }    }
     delti[theta]=delts;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    return res; 
   if (stepm<=12) stepsize=1;    
    }
   agelim=AGESUP;  
    double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   hstepm=1;  {
   hstepm=hstepm/stepm;    int i;
   yp1=modf(dateintmean,&yp);    int l=1, lmax=20;
   anprojmean=yp;    double k1,k2,k3,k4,res,fx;
   yp2=modf((yp1*12),&yp);    double p2[MAXPARM+1];
   mprojmean=yp;    int k;
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;    fx=func(x);
   if(jprojmean==0) jprojmean=1;    for (k=1; k<=2; k++) {
   if(mprojmean==0) jprojmean=1;      for (i=1;i<=npar;i++) p2[i]=x[i];
        p2[thetai]=x[thetai]+delti[thetai]/k;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        k1=func(p2)-fx;
   for(cptcov=1;cptcov<=i2;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      p2[thetai]=x[thetai]+delti[thetai]/k;
       k=k+1;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       fprintf(ficresf,"\n#******");      k2=func(p2)-fx;
       for(j=1;j<=cptcoveff;j++) {    
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      p2[thetai]=x[thetai]-delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       fprintf(ficresf,"******\n");      k3=func(p2)-fx;
       fprintf(ficresf,"# StartingAge FinalAge");    
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      p2[thetai]=x[thetai]-delti[thetai]/k;
            p2[thetaj]=x[thetaj]-delti[thetaj]/k;
            k4=func(p2)-fx;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         fprintf(ficresf,"\n");  #ifdef DEBUG
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);        printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  #endif
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    }
           nhstepm = nhstepm/hstepm;    return res;
            }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;  /************** Inverse of matrix **************/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    void ludcmp(double **a, int n, int *indx, double *d) 
          { 
           for (h=0; h<=nhstepm; h++){    int i,imax,j,k; 
             if (h==(int) (calagedate+YEARM*cpt)) {    double big,dum,sum,temp; 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    double *vv; 
             }   
             for(j=1; j<=nlstate+ndeath;j++) {    vv=vector(1,n); 
               kk1=0.;kk2=0;    *d=1.0; 
               for(i=1; i<=nlstate;i++) {                  for (i=1;i<=n;i++) { 
                 if (mobilav==1)      big=0.0; 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      for (j=1;j<=n;j++) 
                 else {        if ((temp=fabs(a[i][j])) > big) big=temp; 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
                 }      vv[i]=1.0/big; 
                    } 
               }    for (j=1;j<=n;j++) { 
               if (h==(int)(calagedate+12*cpt)){      for (i=1;i<j;i++) { 
                 fprintf(ficresf," %.3f", kk1);        sum=a[i][j]; 
                                for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
               }        a[i][j]=sum; 
             }      } 
           }      big=0.0; 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      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) { 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          big=dum; 
           imax=i; 
   fclose(ficresf);        } 
 }      } 
 /************** Forecasting ******************/      if (j != imax) { 
 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 (k=1;k<=n;k++) { 
            dum=a[imax][k]; 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          a[imax][k]=a[j][k]; 
   int *popage;          a[j][k]=dum; 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        } 
   double *popeffectif,*popcount;        *d = -(*d); 
   double ***p3mat,***tabpop,***tabpopprev;        vv[imax]=vv[j]; 
   char filerespop[FILENAMELENGTH];      } 
       indx[j]=imax; 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (a[j][j] == 0.0) a[j][j]=TINY; 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (j != n) { 
   agelim=AGESUP;        dum=1.0/(a[j][j]); 
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
        } 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    } 
      free_vector(vv,1,n);  /* Doesn't work */
    ;
   strcpy(filerespop,"pop");  } 
   strcat(filerespop,fileres);  
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  void lubksb(double **a, int n, int *indx, double b[]) 
     printf("Problem with forecast resultfile: %s\n", filerespop);  { 
   }    int i,ii=0,ip,j; 
   printf("Computing forecasting: result on file '%s' \n", filerespop);    double sum; 
    
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
   if (mobilav==1) {      sum=b[ip]; 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      b[ip]=b[i]; 
     movingaverage(agedeb, fage, ageminpar, mobaverage);      if (ii) 
   }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
   stepsize=(int) (stepm+YEARM-1)/YEARM;      b[i]=sum; 
   if (stepm<=12) stepsize=1;    } 
      for (i=n;i>=1;i--) { 
   agelim=AGESUP;      sum=b[i]; 
        for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   hstepm=1;      b[i]=sum/a[i][i]; 
   hstepm=hstepm/stepm;    } 
    } 
   if (popforecast==1) {  
     if((ficpop=fopen(popfile,"r"))==NULL) {  void pstamp(FILE *fichier)
       printf("Problem with population file : %s\n",popfile);exit(0);  {
     }    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     popage=ivector(0,AGESUP);  }
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);  /************ Frequencies ********************/
      void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
     i=1;    {  /* Some frequencies */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    
        int i, m, jk, j1, bool, z1,j;
     imx=i;    int first;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    double ***freq; /* Frequencies */
   }    double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
   for(cptcov=1;cptcov<=i2;cptcov++){    char fileresp[FILENAMELENGTH];
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    
       k=k+1;    pp=vector(1,nlstate);
       fprintf(ficrespop,"\n#******");    prop=matrix(1,nlstate,iagemin,iagemax+3);
       for(j=1;j<=cptcoveff;j++) {    strcpy(fileresp,"p");
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcat(fileresp,fileres);
       }    if((ficresp=fopen(fileresp,"w"))==NULL) {
       fprintf(ficrespop,"******\n");      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficrespop,"# Age");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      exit(0);
       if (popforecast==1)  fprintf(ficrespop," [Population]");    }
          freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
       for (cpt=0; cpt<=0;cpt++) {    j1=0;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      
            j=cptcoveff;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;    first=1;
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
           oldm=oldms;savm=savms;    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /*    j1++; */
            for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
           for (h=0; h<=nhstepm; h++){        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
             if (h==(int) (calagedate+YEARM*cpt)) {          scanf("%d", i);*/
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        for (i=-5; i<=nlstate+ndeath; i++)  
             }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
             for(j=1; j<=nlstate+ndeath;j++) {            for(m=iagemin; m <= iagemax+3; m++)
               kk1=0.;kk2=0;              freq[i][jk][m]=0;
               for(i=1; i<=nlstate;i++) {                      
                 if (mobilav==1)        for (i=1; i<=nlstate; i++)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          for(m=iagemin; m <= iagemax+3; m++)
                 else {            prop[i][m]=0;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        
                 }        dateintsum=0;
               }        k2cpt=0;
               if (h==(int)(calagedate+12*cpt)){        for (i=1; i<=imx; i++) {
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          bool=1;
                   /*fprintf(ficrespop," %.3f", kk1);          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/            for (z1=1; z1<=cptcoveff; z1++)       
               }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
             }                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
             for(i=1; i<=nlstate;i++){                bool=0;
               kk1=0.;                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
                 for(j=1; j<=nlstate;j++){                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
                 }                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];              } 
             }          }
    
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          if (bool==1){
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);            for(m=firstpass; m<=lastpass; m++){
           }              k2=anint[m][i]+(mint[m][i]/12.);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
         }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                  if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   /******/                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                  }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){                
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           nhstepm = nhstepm/hstepm;                  dateintsum=dateintsum+k2;
                            k2cpt++;
           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) (calagedate+YEARM*cpt)) {        } /* end i */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);         
             }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
             for(j=1; j<=nlstate+ndeath;j++) {        pstamp(ficresp);
               kk1=0.;kk2=0;        if  (cptcovn>0) {
               for(i=1; i<=nlstate;i++) {                        fprintf(ficresp, "\n#********** Variable "); 
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               }          fprintf(ficresp, "**********\n#");
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);          fprintf(ficlog, "\n#********** Variable "); 
             }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           }          fprintf(ficlog, "**********\n#");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
         }        for(i=1; i<=nlstate;i++) 
       }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
    }        fprintf(ficresp, "\n");
   }        
          for(i=iagemin; i <= iagemax+3; i++){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          if(i==iagemax+3){
             fprintf(ficlog,"Total");
   if (popforecast==1) {          }else{
     free_ivector(popage,0,AGESUP);            if(first==1){
     free_vector(popeffectif,0,AGESUP);              first=0;
     free_vector(popcount,0,AGESUP);              printf("See log file for details...\n");
   }            }
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            fprintf(ficlog,"Age %d", i);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
   fclose(ficrespop);          for(jk=1; jk <=nlstate ; jk++){
 }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
 /***********************************************/          }
 /**************** Main Program *****************/          for(jk=1; jk <=nlstate ; jk++){
 /***********************************************/            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
 int main(int argc, char *argv[])            if(pp[jk]>=1.e-10){
 {              if(first==1){
                 printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;              }
   double agedeb, agefin,hf;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;            }else{
               if(first==1)
   double fret;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   double **xi,tmp,delta;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
   double dum; /* Dummy variable */          }
   double ***p3mat;  
   int *indx;          for(jk=1; jk <=nlstate ; jk++){
   char line[MAXLINE], linepar[MAXLINE];            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   char title[MAXLINE];              pp[jk] += freq[jk][m][i];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          }       
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
              pos += pp[jk];
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];            posprop += prop[jk][i];
           }
   char filerest[FILENAMELENGTH];          for(jk=1; jk <=nlstate ; jk++){
   char fileregp[FILENAMELENGTH];            if(pos>=1.e-5){
   char popfile[FILENAMELENGTH];              if(first==1)
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   int firstobs=1, lastobs=10;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   int sdeb, sfin; /* Status at beginning and end */            }else{
   int c,  h , cpt,l;              if(first==1)
   int ju,jl, mi;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            }
   int mobilav=0,popforecast=0;            if( i <= iagemax){
   int hstepm, nhstepm;              if(pos>=1.e-5){
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
   double bage, fage, age, agelim, agebase;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   double ftolpl=FTOL;              }
   double **prlim;              else
   double *severity;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   double ***param; /* Matrix of parameters */            }
   double  *p;          }
   double **matcov; /* Matrix of covariance */          
   double ***delti3; /* Scale */          for(jk=-1; jk <=nlstate+ndeath; jk++)
   double *delti; /* Scale */            for(m=-1; m <=nlstate+ndeath; m++)
   double ***eij, ***vareij;              if(freq[jk][m][i] !=0 ) {
   double **varpl; /* Variances of prevalence limits by age */              if(first==1)
   double *epj, vepp;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   double kk1, kk2;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;              }
            if(i <= iagemax)
             fprintf(ficresp,"\n");
   char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";          if(first==1)
   char *alph[]={"a","a","b","c","d","e"}, str[4];            printf("Others in log...\n");
           fprintf(ficlog,"\n");
         }
   char z[1]="c", occ;        /*}*/
 #include <sys/time.h>    }
 #include <time.h>    dateintmean=dateintsum/k2cpt; 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];   
      fclose(ficresp);
   /* long total_usecs;    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   struct timeval start_time, end_time;    free_vector(pp,1,nlstate);
      free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    /* End of Freq */
   getcwd(pathcd, size);  }
   
   printf("\n%s",version);  /************ Prevalence ********************/
   if(argc <=1){  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)
     printf("\nEnter the parameter file name: ");  {  
     scanf("%s",pathtot);    /* 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).
   else{       We still use firstpass and lastpass as another selection.
     strcpy(pathtot,argv[1]);    */
   }   
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    int i, m, jk, j1, bool, z1,j;
   /*cygwin_split_path(pathtot,path,optionfile);  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    double **prop;
   /* cutv(path,optionfile,pathtot,'\\');*/    double posprop; 
     double  y2; /* in fractional years */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    int iagemin, iagemax;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    int first; /** to stop verbosity which is redirected to log file */
   chdir(path);  
   replace(pathc,path);    iagemin= (int) agemin;
     iagemax= (int) agemax;
 /*-------- arguments in the command line --------*/    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
   strcpy(fileres,"r");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   strcat(fileres, optionfilefiname);    j1=0;
   strcat(fileres,".txt");    /* Other files have txt extension */    
     /*j=cptcoveff;*/
   /*---------arguments file --------*/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    first=1;
     printf("Problem with optionfile %s\n",optionfile);    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
     goto end;      /*for(i1=1; i1<=ncodemax[k1];i1++){
   }        j1++;*/
         
   strcpy(filereso,"o");        for (i=1; i<=nlstate; i++)  
   strcat(filereso,fileres);          for(m=iagemin; m <= iagemax+3; m++)
   if((ficparo=fopen(filereso,"w"))==NULL) {            prop[i][m]=0.0;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;       
   }        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
   /* Reads comments: lines beginning with '#' */          if  (cptcovn>0) {
   while((c=getc(ficpar))=='#' && c!= EOF){            for (z1=1; z1<=cptcoveff; z1++) 
     ungetc(c,ficpar);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     fgets(line, MAXLINE, ficpar);                bool=0;
     puts(line);          } 
     fputs(line,ficparo);          if (bool==1) { 
   }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   ungetc(c,ficpar);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   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);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   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);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   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((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); 
 while((c=getc(ficpar))=='#' && c!= EOF){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     ungetc(c,ficpar);                  /*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]]);*/
     fgets(line, MAXLINE, ficpar);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     puts(line);                  prop[s[m][i]][iagemax+3] += weight[i]; 
     fputs(line,ficparo);                } 
   }              }
   ungetc(c,ficpar);            } /* end selection of waves */
            }
            }
   covar=matrix(0,NCOVMAX,1,n);        for(i=iagemin; i <= iagemax+3; i++){  
   cptcovn=0;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;            posprop += prop[jk][i]; 
           } 
   ncovmodel=2+cptcovn;          
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          for(jk=1; jk <=nlstate ; jk++){     
              if( i <=  iagemax){ 
   /* Read guess parameters */              if(posprop>=1.e-5){ 
   /* Reads comments: lines beginning with '#' */                probs[i][jk][j1]= prop[jk][i]/posprop;
   while((c=getc(ficpar))=='#' && c!= EOF){              } else{
     ungetc(c,ficpar);                if(first==1){
     fgets(line, MAXLINE, ficpar);                  first=0;
     puts(line);                  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]);
     fputs(line,ficparo);                }
   }              }
   ungetc(c,ficpar);            } 
            }/* end jk */ 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        }/* end i */ 
     for(i=1; i <=nlstate; i++)      /*} *//* end i1 */
     for(j=1; j <=nlstate+ndeath-1; j++){    } /* end j1 */
       fscanf(ficpar,"%1d%1d",&i1,&j1);    
       fprintf(ficparo,"%1d%1d",i1,j1);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       printf("%1d%1d",i,j);    /*free_vector(pp,1,nlstate);*/
       for(k=1; k<=ncovmodel;k++){    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
         fscanf(ficpar," %lf",&param[i][j][k]);  }  /* End of prevalence */
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);  /************* Waves Concatenation ***************/
       }  
       fscanf(ficpar,"\n");  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
       printf("\n");  {
       fprintf(ficparo,"\n");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     }       Death is a valid wave (if date is known).
         mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
   p=param[1][1];       */
    
   /* Reads comments: lines beginning with '#' */    int i, mi, m;
   while((c=getc(ficpar))=='#' && c!= EOF){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     ungetc(c,ficpar);       double sum=0., jmean=0.;*/
     fgets(line, MAXLINE, ficpar);    int first;
     puts(line);    int j, k=0,jk, ju, jl;
     fputs(line,ficparo);    double sum=0.;
   }    first=0;
   ungetc(c,ficpar);    jmin=100000;
     jmax=-1;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    jmean=0.;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    for(i=1; i<=imx; i++){
   for(i=1; i <=nlstate; i++){      mi=0;
     for(j=1; j <=nlstate+ndeath-1; j++){      m=firstpass;
       fscanf(ficpar,"%1d%1d",&i1,&j1);      while(s[m][i] <= nlstate){
       printf("%1d%1d",i,j);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       fprintf(ficparo,"%1d%1d",i1,j1);          mw[++mi][i]=m;
       for(k=1; k<=ncovmodel;k++){        if(m >=lastpass)
         fscanf(ficpar,"%le",&delti3[i][j][k]);          break;
         printf(" %le",delti3[i][j][k]);        else
         fprintf(ficparo," %le",delti3[i][j][k]);          m++;
       }      }/* end while */
       fscanf(ficpar,"\n");      if (s[m][i] > nlstate){
       printf("\n");        mi++;     /* Death is another wave */
       fprintf(ficparo,"\n");        /* if(mi==0)  never been interviewed correctly before death */
     }           /* Only death is a correct wave */
   }        mw[mi][i]=m;
   delti=delti3[1][1];      }
    
   /* Reads comments: lines beginning with '#' */      wav[i]=mi;
   while((c=getc(ficpar))=='#' && c!= EOF){      if(mi==0){
     ungetc(c,ficpar);        nbwarn++;
     fgets(line, MAXLINE, ficpar);        if(first==0){
     puts(line);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     fputs(line,ficparo);          first=1;
   }        }
   ungetc(c,ficpar);        if(first==1){
            fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
   matcov=matrix(1,npar,1,npar);        }
   for(i=1; i <=npar; i++){      } /* end mi==0 */
     fscanf(ficpar,"%s",&str);    } /* End individuals */
     printf("%s",str);  
     fprintf(ficparo,"%s",str);    for(i=1; i<=imx; i++){
     for(j=1; j <=i; j++){      for(mi=1; mi<wav[i];mi++){
       fscanf(ficpar," %le",&matcov[i][j]);        if (stepm <=0)
       printf(" %.5le",matcov[i][j]);          dh[mi][i]=1;
       fprintf(ficparo," %.5le",matcov[i][j]);        else{
     }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     fscanf(ficpar,"\n");            if (agedc[i] < 2*AGESUP) {
     printf("\n");              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     fprintf(ficparo,"\n");              if(j==0) j=1;  /* Survives at least one month after exam */
   }              else if(j<0){
   for(i=1; i <=npar; i++)                nberr++;
     for(j=i+1;j<=npar;j++)                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]);
       matcov[i][j]=matcov[j][i];                j=1; /* Temporary Dangerous patch */
                    printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
   printf("\n");                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);
               }
     /*-------- Rewriting paramater file ----------*/              k=k+1;
      strcpy(rfileres,"r");    /* "Rparameterfile */              if (j >= jmax){
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/                jmax=j;
      strcat(rfileres,".");    /* */                ijmax=i;
      strcat(rfileres,optionfilext);    /* Other files have txt extension */              }
     if((ficres =fopen(rfileres,"w"))==NULL) {              if (j <= jmin){
       printf("Problem writing new parameter file: %s\n", fileres);goto end;                jmin=j;
     }                ijmin=i;
     fprintf(ficres,"#%s\n",version);              }
                  sum=sum+j;
     /*-------- data file ----------*/              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     if((fic=fopen(datafile,"r"))==NULL)    {              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       printf("Problem with datafile: %s\n", datafile);goto end;            }
     }          }
           else{
     n= lastobs;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     severity = vector(1,maxwav);  /*        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]); */
     outcome=imatrix(1,maxwav+1,1,n);  
     num=ivector(1,n);            k=k+1;
     moisnais=vector(1,n);            if (j >= jmax) {
     annais=vector(1,n);              jmax=j;
     moisdc=vector(1,n);              ijmax=i;
     andc=vector(1,n);            }
     agedc=vector(1,n);            else if (j <= jmin){
     cod=ivector(1,n);              jmin=j;
     weight=vector(1,n);              ijmin=i;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            }
     mint=matrix(1,maxwav,1,n);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     anint=matrix(1,maxwav,1,n);            /*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]);*/
     s=imatrix(1,maxwav+1,1,n);            if(j<0){
     adl=imatrix(1,maxwav+1,1,n);                  nberr++;
     tab=ivector(1,NCOVMAX);              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]);
     ncodemax=ivector(1,8);              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]);
             }
     i=1;            sum=sum+j;
     while (fgets(line, MAXLINE, fic) != NULL)    {          }
       if ((i >= firstobs) && (i <=lastobs)) {          jk= j/stepm;
                  jl= j -jk*stepm;
         for (j=maxwav;j>=1;j--){          ju= j -(jk+1)*stepm;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           strcpy(line,stra);            if(jl==0){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              dh[mi][i]=jk;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=0;
         }            }else{ /* We want a negative bias in order to only have interpolation ie
                            * to avoid the price of an extra matrix product in likelihood */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              dh[mi][i]=jk+1;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=ju;
             }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          }else{
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            if(jl <= -ju){
               dh[mi][i]=jk;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=jl;       /* bias is positive if real duration
         for (j=ncovcol;j>=1;j--){                                   * is higher than the multiple of stepm and negative otherwise.
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                                   */
         }            }
         num[i]=atol(stra);            else{
                      dh[mi][i]=jk+1;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){              bh[mi][i]=ju;
           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(dh[mi][i]==0){
         i=i+1;              dh[mi][i]=1; /* At least one step */
       }              bh[mi][i]=ju; /* At least one step */
     }              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
     /* printf("ii=%d", ij);            }
        scanf("%d",i);*/          } /* end if mle */
   imx=i-1; /* Number of individuals */        }
       } /* end wave */
   /* for (i=1; i<=imx; i++){    }
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    jmean=sum/k;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    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);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    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);
     }*/   }
    /*  for (i=1; i<=imx; i++){  
      if (s[4][i]==9)  s[4][i]=-1;  /*********** Tricode ****************************/
      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]));}*/  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
    {
      /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   /* Calculation of the number of parameter from char model*/    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   Tvar=ivector(1,15);     * Boring subroutine which should only output nbcode[Tvar[j]][k]
   Tprod=ivector(1,15);     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
   Tvaraff=ivector(1,15);     * nbcode[Tvar[j]][1]= 
   Tvard=imatrix(1,15,1,2);    */
   Tage=ivector(1,15);        
        int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   if (strlen(model) >1){    int modmaxcovj=0; /* Modality max of covariates j */
     j=0, j1=0, k1=1, k2=1;    int cptcode=0; /* Modality max of covariates j */
     j=nbocc(model,'+');    int modmincovj=0; /* Modality min of covariates j */
     j1=nbocc(model,'*');  
     cptcovn=j+1;  
     cptcovprod=j1;    cptcoveff=0; 
       
     strcpy(modelsav,model);    for (k=-1; k < maxncov; k++) Ndum[k]=0;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
       printf("Error. Non available option model=%s ",model);  
       goto end;    /* Loop on covariates without age and products */
     }    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
          for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
     for(i=(j+1); i>=1;i--){                                 modality of this covariate Vj*/ 
       cutv(stra,strb,modelsav,'+');        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                                      * If product of Vn*Vm, still boolean *:
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
       /*scanf("%d",i);*/                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
       if (strchr(strb,'*')) {        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
         cutv(strd,strc,strb,'*');                                        modality of the nth covariate of individual i. */
         if (strcmp(strc,"age")==0) {        if (ij > modmaxcovj)
           cptcovprod--;          modmaxcovj=ij; 
           cutv(strb,stre,strd,'V');        else if (ij < modmincovj) 
           Tvar[i]=atoi(stre);          modmincovj=ij; 
           cptcovage++;        if ((ij < -1) && (ij > NCOVMAX)){
             Tage[cptcovage]=i;          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
             /*printf("stre=%s ", stre);*/          exit(1);
         }        }else
         else if (strcmp(strd,"age")==0) {        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
           cptcovprod--;        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
           cutv(strb,stre,strc,'V');        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           Tvar[i]=atoi(stre);        /* getting the maximum value of the modality of the covariate
           cptcovage++;           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
           Tage[cptcovage]=i;           female is 1, then modmaxcovj=1.*/
         }      }
         else {      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
           cutv(strb,stre,strc,'V');      cptcode=modmaxcovj;
           Tvar[i]=ncovcol+k1;      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
           cutv(strb,strc,strd,'V');     /*for (i=0; i<=cptcode; i++) {*/
           Tprod[k1]=i;      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
           Tvard[k1][1]=atoi(strc);        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
           Tvard[k1][2]=atoi(stre);        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           Tvar[cptcovn+k2]=Tvard[k1][1];          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        }
           for (k=1; k<=lastobs;k++)        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
           k1++;      } /* Ndum[-1] number of undefined modalities */
           k2=k2+2;  
         }      /* 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 */
       else {      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/         modmincovj=3; modmaxcovj = 7;
        /*  scanf("%d",i);*/         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
       cutv(strd,strc,strb,'V');         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
       Tvar[i]=atoi(strc);         variables V1_1 and V1_2.
       }         nbcode[Tvar[j]][ij]=k;
       strcpy(modelsav,stra);           nbcode[Tvar[j]][1]=0;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);         nbcode[Tvar[j]][2]=1;
         scanf("%d",i);*/         nbcode[Tvar[j]][3]=2;
     }      */
 }      ij=1; /* ij is similar to i but can jumps over null modalities */
        for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
   printf("cptcovprod=%d ", cptcovprod);          /*recode from 0 */
   scanf("%d ",i);*/          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
     fclose(fic);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                                        k is a modality. If we have model=V1+V1*sex 
     /*  if(mle==1){*/                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     if (weightopt != 1) { /* Maximisation without weights*/            ij++;
       for(i=1;i<=n;i++) weight[i]=1.0;          }
     }          if (ij > ncodemax[j]) break; 
     /*-calculation of age at interview from date of interview and age at death -*/        }  /* end of loop on */
     agev=matrix(1,maxwav,1,imx);      } /* end of loop on modality */ 
     } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     for (i=1; i<=imx; i++) {    
       for(m=2; (m<= maxwav); m++) {   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    
          anint[m][i]=9999;    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
          s[m][i]=-1;     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
        }     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;     Ndum[ij]++; 
       }   } 
     }  
    ij=1;
     for (i=1; i<=imx; i++)  {   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
       for(m=1; (m<= maxwav); m++){     if((Ndum[i]!=0) && (i<=ncovcol)){
         if(s[m][i] >0){       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
           if (s[m][i] >= nlstate+1) {       Tvaraff[ij]=i; /*For printing (unclear) */
             if(agedc[i]>0)       ij++;
               if(moisdc[i]!=99 && andc[i]!=9999)     }else
                 agev[m][i]=agedc[i];         Tvaraff[ij]=0;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/   }
            else {   ij--;
               if (andc[i]!=9999){   cptcoveff=ij; /*Number of total covariates*/
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;  }
               }  
             }  
           }  /*********** Health Expectancies ****************/
           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]);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;  {
             else if(agev[m][i] <agemin){    /* Health expectancies, no variances */
               agemin=agev[m][i];    int i, j, nhstepm, hstepm, h, nstepm;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    int nhstepma, nstepma; /* Decreasing with age */
             }    double age, agelim, hf;
             else if(agev[m][i] >agemax){    double ***p3mat;
               agemax=agev[m][i];    double eip;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }    pstamp(ficreseij);
             /*agev[m][i]=anint[m][i]-annais[i];*/    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
             /*   agev[m][i] = age[i]+2*m;*/    fprintf(ficreseij,"# Age");
           }    for(i=1; i<=nlstate;i++){
           else { /* =9 */      for(j=1; j<=nlstate;j++){
             agev[m][i]=1;        fprintf(ficreseij," e%1d%1d ",i,j);
             s[m][i]=-1;      }
           }      fprintf(ficreseij," e%1d. ",i);
         }    }
         else /*= 0 Unknown */    fprintf(ficreseij,"\n");
           agev[m][i]=1;  
       }    
        if(estepm < stepm){
     }      printf ("Problem %d lower than %d\n",estepm, stepm);
     for (i=1; i<=imx; i++)  {    }
       for(m=1; (m<= maxwav); m++){    else  hstepm=estepm;   
         if (s[m][i] > (nlstate+ndeath)) {    /* We compute the life expectancy from trapezoids spaced every estepm months
           printf("Error: Wrong value in nlstate or ndeath\n");       * This is mainly to measure the difference between two models: for example
           goto end;     * if stepm=24 months pijx are given only every 2 years and by summing them
         }     * we are calculating an estimate of the Life Expectancy assuming a linear 
       }     * progression in between and thus overestimating or underestimating according
     }     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
     free_vector(severity,1,maxwav);     * curvature will be obtained if estepm is as small as stepm. */
     free_imatrix(outcome,1,maxwav+1,1,n);  
     free_vector(moisnais,1,n);    /* For example we decided to compute the life expectancy with the smallest unit */
     free_vector(annais,1,n);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     /* free_matrix(mint,1,maxwav,1,n);       nhstepm is the number of hstepm from age to agelim 
        free_matrix(anint,1,maxwav,1,n);*/       nstepm is the number of stepm from age to agelin. 
     free_vector(moisdc,1,n);       Look at hpijx to understand the reason of that which relies in memory size
     free_vector(andc,1,n);       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           survival function given by stepm (the optimization length). Unfortunately it
     wav=ivector(1,imx);       means that if the survival funtion is printed only each two years of age and if
     dh=imatrix(1,lastpass-firstpass+1,1,imx);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);       results. So we changed our mind and took the option of the best precision.
        */
     /* Concatenates waves */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
     agelim=AGESUP;
     /* If stepm=6 months */
       Tcode=ivector(1,100);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       ncodemax[1]=1;      
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  /* nhstepm age range expressed in number of stepm */
          nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
    codtab=imatrix(1,100,1,10);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
    h=0;    /* if (stepm >= YEARM) hstepm=1;*/
    m=pow(2,cptcoveff);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){    for (age=bage; age<=fage; age ++){ 
        for(j=1; j <= ncodemax[k]; j++){      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
            h++;      /* if (stepm >= YEARM) hstepm=1;*/
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/  
          }      /* 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 */
    }      
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       codtab[1][2]=1;codtab[2][2]=2; */      
    /* for(i=1; i <=m ;i++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(k=1; k <=cptcovn; k++){      
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);      printf("%d|",(int)age);fflush(stdout);
       }      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       printf("\n");      
       }      /* Computing expectancies */
       scanf("%d",i);*/      for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate;j++)
    /* Calculates basic frequencies. Computes observed prevalence at single age          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
        and prints on file fileres'p'. */            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
                /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
      
     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 */      fprintf(ficreseij,"%3.0f",age );
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(i=1; i<=nlstate;i++){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        eip=0;
              for(j=1; j<=nlstate;j++){
     /* For Powell, parameters are in a vector p[] starting at p[1]          eip +=eij[i][j][(int)age];
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        }
         fprintf(ficreseij,"%9.4f", eip );
     if(mle==1){      }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      fprintf(ficreseij,"\n");
     }      
        }
     /*--------- results files --------------*/    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     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);    printf("\n");
      fprintf(ficlog,"\n");
     
    jk=1;  }
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
    for(i=1,jk=1; i <=nlstate; i++){  
      for(k=1; k <=(nlstate+ndeath); k++){  {
        if (k != i)    /* Covariances of health expectancies eij and of total life expectancies according
          {     to initial status i, ei. .
            printf("%d%d ",i,k);    */
            fprintf(ficres,"%1d%1d ",i,k);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
            for(j=1; j <=ncovmodel; j++){    int nhstepma, nstepma; /* Decreasing with age */
              printf("%f ",p[jk]);    double age, agelim, hf;
              fprintf(ficres,"%f ",p[jk]);    double ***p3matp, ***p3matm, ***varhe;
              jk++;    double **dnewm,**doldm;
            }    double *xp, *xm;
            printf("\n");    double **gp, **gm;
            fprintf(ficres,"\n");    double ***gradg, ***trgradg;
          }    int theta;
      }  
    }    double eip, vip;
  if(mle==1){  
     /* Computing hessian and covariance matrix */    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     ftolhess=ftol; /* Usually correct */    xp=vector(1,npar);
     hesscov(matcov, p, npar, delti, ftolhess, func);    xm=vector(1,npar);
  }    dnewm=matrix(1,nlstate*nlstate,1,npar);
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     printf("# Scales (for hessian or gradient estimation)\n");    
      for(i=1,jk=1; i <=nlstate; i++){    pstamp(ficresstdeij);
       for(j=1; j <=nlstate+ndeath; j++){    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
         if (j!=i) {    fprintf(ficresstdeij,"# Age");
           fprintf(ficres,"%1d%1d",i,j);    for(i=1; i<=nlstate;i++){
           printf("%1d%1d",i,j);      for(j=1; j<=nlstate;j++)
           for(k=1; k<=ncovmodel;k++){        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
             printf(" %.5e",delti[jk]);      fprintf(ficresstdeij," e%1d. ",i);
             fprintf(ficres," %.5e",delti[jk]);    }
             jk++;    fprintf(ficresstdeij,"\n");
           }  
           printf("\n");    pstamp(ficrescveij);
           fprintf(ficres,"\n");    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
         }    fprintf(ficrescveij,"# Age");
       }    for(i=1; i<=nlstate;i++)
      }      for(j=1; j<=nlstate;j++){
            cptj= (j-1)*nlstate+i;
     k=1;        for(i2=1; i2<=nlstate;i2++)
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");          for(j2=1; j2<=nlstate;j2++){
     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");            cptj2= (j2-1)*nlstate+i2;
     for(i=1;i<=npar;i++){            if(cptj2 <= cptj)
       /*  if (k>nlstate) k=1;              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
       i1=(i-1)/(ncovmodel*nlstate)+1;          }
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      }
       printf("%s%d%d",alph[k],i1,tab[i]);*/    fprintf(ficrescveij,"\n");
       fprintf(ficres,"%3d",i);    
       printf("%3d",i);    if(estepm < stepm){
       for(j=1; j<=i;j++){      printf ("Problem %d lower than %d\n",estepm, stepm);
         fprintf(ficres," %.5e",matcov[i][j]);    }
         printf(" %.5e",matcov[i][j]);    else  hstepm=estepm;   
       }    /* We compute the life expectancy from trapezoids spaced every estepm months
       fprintf(ficres,"\n");     * This is mainly to measure the difference between two models: for example
       printf("\n");     * if stepm=24 months pijx are given only every 2 years and by summing them
       k++;     * we are calculating an estimate of the Life Expectancy assuming a linear 
     }     * progression in between and thus overestimating or underestimating according
         * to the curvature of the survival function. If, for the same date, we 
     while((c=getc(ficpar))=='#' && c!= EOF){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       ungetc(c,ficpar);     * to compare the new estimate of Life expectancy with the same linear 
       fgets(line, MAXLINE, ficpar);     * hypothesis. A more precise result, taking into account a more precise
       puts(line);     * curvature will be obtained if estepm is as small as stepm. */
       fputs(line,ficparo);  
     }    /* For example we decided to compute the life expectancy with the smallest unit */
     ungetc(c,ficpar);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     estepm=0;       nhstepm is the number of hstepm from age to agelim 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);       nstepm is the number of stepm from age to agelin. 
     if (estepm==0 || estepm < stepm) estepm=stepm;       Look at hpijx to understand the reason of that which relies in memory size
     if (fage <= 2) {       and note for a fixed period like estepm months */
       bage = ageminpar;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       fage = agemaxpar;       survival function given by stepm (the optimization length). Unfortunately it
     }       means that if the survival funtion is printed only each two years of age and if
           you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");       results. So we changed our mind and took the option of the best precision.
     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);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    
     while((c=getc(ficpar))=='#' && c!= EOF){    /* If stepm=6 months */
     ungetc(c,ficpar);    /* nhstepm age range expressed in number of stepm */
     fgets(line, MAXLINE, ficpar);    agelim=AGESUP;
     puts(line);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     fputs(line,ficparo);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   }    /* if (stepm >= YEARM) hstepm=1;*/
   ungetc(c,ficpar);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
          trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     ungetc(c,ficpar);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
     fgets(line, MAXLINE, ficpar);  
     puts(line);    for (age=bage; age<=fage; age ++){ 
     fputs(line,ficparo);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   ungetc(c,ficpar);      /* if (stepm >= YEARM) hstepm=1;*/
        nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      /* If stepm=6 months */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   fscanf(ficpar,"pop_based=%d\n",&popbased);      
   fprintf(ficparo,"pop_based=%d\n",popbased);        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   fprintf(ficres,"pop_based=%d\n",popbased);    
        /* Computing  Variances of health expectancies */
   while((c=getc(ficpar))=='#' && c!= EOF){      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     ungetc(c,ficpar);         decrease memory allocation */
     fgets(line, MAXLINE, ficpar);      for(theta=1; theta <=npar; theta++){
     puts(line);        for(i=1; i<=npar; i++){ 
     fputs(line,ficparo);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }          xm[i] = x[i] - (i==theta ?delti[theta]:0);
   ungetc(c,ficpar);        }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
   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);        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
 while((c=getc(ficpar))=='#' && c!= EOF){              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     ungetc(c,ficpar);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
     fgets(line, MAXLINE, ficpar);            }
     puts(line);          }
     fputs(line,ficparo);        }
   }       
   ungetc(c,ficpar);        for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          }
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      }/* End theta */
       
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      
       for(h=0; h<=nhstepm-1; h++)
 /*------------ gnuplot -------------*/        for(j=1; j<=nlstate*nlstate;j++)
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);          for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
 /*------------ free_vector  -------------*/      
  chdir(path);  
         for(ij=1;ij<=nlstate*nlstate;ij++)
  free_ivector(wav,1,imx);        for(ji=1;ji<=nlstate*nlstate;ji++)
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          varhe[ij][ji][(int)age] =0.;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    
  free_ivector(num,1,n);       printf("%d|",(int)age);fflush(stdout);
  free_vector(agedc,1,n);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/       for(h=0;h<=nhstepm-1;h++){
  fclose(ficparo);        for(k=0;k<=nhstepm-1;k++){
  fclose(ficres);          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]);
 /*--------- index.htm --------*/          for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
        }
   /*--------------- Prevalence limit --------------*/  
        /* Computing expectancies */
   strcpy(filerespl,"pl");      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   strcat(filerespl,fileres);      for(i=1; i<=nlstate;i++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        for(j=1; j<=nlstate;j++)
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   }            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            
   fprintf(ficrespl,"#Prevalence limit\n");            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          }
   fprintf(ficrespl,"\n");  
        fprintf(ficresstdeij,"%3.0f",age );
   prlim=matrix(1,nlstate,1,nlstate);      for(i=1; i<=nlstate;i++){
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        eip=0.;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        vip=0.;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1; j<=nlstate;j++){
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          eip += eij[i][j][(int)age];
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   k=0;            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   agebase=ageminpar;          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
   agelim=agemaxpar;        }
   ftolpl=1.e-10;        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   i1=cptcoveff;      }
   if (cptcovn < 1){i1=1;}      fprintf(ficresstdeij,"\n");
   
   for(cptcov=1;cptcov<=i1;cptcov++){      fprintf(ficrescveij,"%3.0f",age );
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(i=1; i<=nlstate;i++)
         k=k+1;        for(j=1; j<=nlstate;j++){
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          cptj= (j-1)*nlstate+i;
         fprintf(ficrespl,"\n#******");          for(i2=1; i2<=nlstate;i2++)
         for(j=1;j<=cptcoveff;j++)            for(j2=1; j2<=nlstate;j2++){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              cptj2= (j2-1)*nlstate+i2;
         fprintf(ficrespl,"******\n");              if(cptj2 <= cptj)
                        fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
         for (age=agebase; age<=agelim; age++){            }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        }
           fprintf(ficrespl,"%.0f",age );      fprintf(ficrescveij,"\n");
           for(i=1; i<=nlstate;i++)     
           fprintf(ficrespl," %.5f", prlim[i][i]);    }
           fprintf(ficrespl,"\n");    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
         }    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       }    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     }    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   fclose(ficrespl);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*------------- h Pij x at various ages ------------*/    printf("\n");
      fprintf(ficlog,"\n");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    free_vector(xm,1,npar);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    free_vector(xp,1,npar);
   }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   printf("Computing pij: result on file '%s' \n", filerespij);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
      free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   stepsize=(int) (stepm+YEARM-1)/YEARM;  }
   /*if (stepm<=24) stepsize=2;*/  
   /************ Variance ******************/
   agelim=AGESUP;  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[])
   hstepm=stepsize*YEARM; /* Every year of age */  {
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    /* Variance of health expectancies */
      /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   k=0;    /* double **newm;*/
   for(cptcov=1;cptcov<=i1;cptcov++){    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
       k=k+1;    int movingaverage();
         fprintf(ficrespij,"\n#****** ");    double **dnewm,**doldm;
         for(j=1;j<=cptcoveff;j++)    double **dnewmp,**doldmp;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int i, j, nhstepm, hstepm, h, nstepm ;
         fprintf(ficrespij,"******\n");    int k;
            double *xp;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    double **gp, **gm;  /* for var eij */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double ***gradg, ***trgradg; /*for var eij */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double **gradgp, **trgradgp; /* for var p point j */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double *gpp, *gmp; /* for var p point j */
           oldm=oldms;savm=savms;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double ***p3mat;
           fprintf(ficrespij,"# Age");    double age,agelim, hf;
           for(i=1; i<=nlstate;i++)    double ***mobaverage;
             for(j=1; j<=nlstate+ndeath;j++)    int theta;
               fprintf(ficrespij," %1d-%1d",i,j);    char digit[4];
           fprintf(ficrespij,"\n");    char digitp[25];
            for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    char fileresprobmorprev[FILENAMELENGTH];
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)    if(popbased==1){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      if(mobilav!=0)
             fprintf(ficrespij,"\n");        strcpy(digitp,"-populbased-mobilav-");
              }      else strcpy(digitp,"-populbased-nomobil-");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
           fprintf(ficrespij,"\n");    else 
         }      strcpy(digitp,"-stablbased-");
     }  
   }    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   fclose(ficrespij);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   /*---------- Forecasting ------------------*/  
   if((stepm == 1) && (strcmp(model,".")==0)){    strcpy(fileresprobmorprev,"prmorprev"); 
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    sprintf(digit,"%-d",ij);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   else{    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     erreur=108;    strcat(fileresprobmorprev,fileres);
     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);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
   /*---------- Health expectancies and variances ------------*/    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
   strcpy(filerest,"t");    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   strcat(filerest,fileres);    pstamp(ficresprobmorprev);
   if((ficrest=fopen(filerest,"w"))==NULL) {    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);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   strcpy(filerese,"e");    }  
   strcat(filerese,fileres);    fprintf(ficresprobmorprev,"\n");
   if((ficreseij=fopen(filerese,"w"))==NULL) {    fprintf(ficgp,"\n# Routine varevsij");
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    /* 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");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
  strcpy(fileresv,"v");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   strcat(fileresv,fileres);    pstamp(ficresvij);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    if(popbased==1)
   }      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    else
   calagedate=-1;      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
   k=0;      for(j=1; j<=nlstate;j++)
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficresvij,"\n");
       k=k+1;  
       fprintf(ficrest,"\n#****** ");    xp=vector(1,npar);
       for(j=1;j<=cptcoveff;j++)    dnewm=matrix(1,nlstate,1,npar);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    doldm=matrix(1,nlstate,1,nlstate);
       fprintf(ficrest,"******\n");    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       fprintf(ficreseij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    gpp=vector(nlstate+1,nlstate+ndeath);
       fprintf(ficreseij,"******\n");    gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       fprintf(ficresvij,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    if(estepm < stepm){
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf ("Problem %d lower than %d\n",estepm, stepm);
       fprintf(ficresvij,"******\n");    }
     else  hstepm=estepm;   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    /* For example we decided to compute the life expectancy with the smallest unit */
       oldm=oldms;savm=savms;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);         nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       Look at function hpijx to understand why (it is linked to memory size questions) */
       oldm=oldms;savm=savms;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);       survival function given by stepm (the optimization length). Unfortunately it
           means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         results. So we changed our mind and took the option of the best precision.
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       fprintf(ficrest,"\n");    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       epj=vector(1,nlstate+1);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       for(age=bage; age <=fage ;age++){      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         if (popbased==1) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
           for(i=1; i<=nlstate;i++)      gp=matrix(0,nhstepm,1,nlstate);
             prlim[i][i]=probs[(int)age][i][k];      gm=matrix(0,nhstepm,1,nlstate);
         }  
          
         fprintf(ficrest," %4.0f",age);      for(theta=1; theta <=npar; theta++){
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];        }
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           epj[nlstate+1] +=epj[j];  
         }        if (popbased==1) {
           if(mobilav ==0){
         for(i=1, vepp=0.;i <=nlstate;i++)            for(i=1; i<=nlstate;i++)
           for(j=1;j <=nlstate;j++)              prlim[i][i]=probs[(int)age][i][ij];
             vepp += vareij[i][j][(int)age];          }else{ /* mobilav */ 
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));            for(i=1; i<=nlstate;i++)
         for(j=1;j <=nlstate;j++){              prlim[i][i]=mobaverage[(int)age][i][ij];
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));          }
         }        }
         fprintf(ficrest,"\n");    
       }        for(j=1; j<= nlstate; j++){
     }          for(h=0; h<=nhstepm; h++){
   }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
 free_matrix(mint,1,maxwav,1,n);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);          }
     free_vector(weight,1,n);        }
   fclose(ficreseij);        /* This for computing probability of death (h=1 means
   fclose(ficresvij);           computed over hstepm matrices product = hstepm*stepm months) 
   fclose(ficrest);           as a weighted average of prlim.
   fclose(ficpar);        */
   free_vector(epj,1,nlstate+1);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gpp[j]=0.; i<= nlstate; i++)
   /*------- Variance limit prevalence------*/              gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
   strcpy(fileresvpl,"vpl");        /* end probability of death */
   strcat(fileresvpl,fileres);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     exit(0);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);   
         if (popbased==1) {
   k=0;          if(mobilav ==0){
   for(cptcov=1;cptcov<=i1;cptcov++){            for(i=1; i<=nlstate;i++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              prlim[i][i]=probs[(int)age][i][ij];
       k=k+1;          }else{ /* mobilav */ 
       fprintf(ficresvpl,"\n#****** ");            for(i=1; i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++)              prlim[i][i]=mobaverage[(int)age][i][ij];
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          }
       fprintf(ficresvpl,"******\n");        }
        
       varpl=matrix(1,nlstate,(int) bage, (int) fage);        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
       oldm=oldms;savm=savms;          for(h=0; h<=nhstepm; h++){
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
  }          }
         }
   fclose(ficresvpl);        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
   /*---------- End : free ----------------*/           as a weighted average of prlim.
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
          /* end probability of death */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        for(j=1; j<= nlstate; j++) /* vareij */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);          for(h=0; h<=nhstepm; h++){
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   free_matrix(agev,1,maxwav,1,imx);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        }
   
   if(erreur >0)      } /* End theta */
     printf("End of Imach with error or warning %d\n",erreur);  
   else   printf("End of Imach\n");      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
        for(h=0; h<=nhstepm; h++) /* veij */
   /* 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);*/        for(j=1; j<=nlstate;j++)
   /*printf("Total time was %d uSec.\n", total_usecs);*/          for(theta=1; theta <=npar; theta++)
   /*------ End -----------*/            trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
  end:        for(theta=1; theta <=npar; theta++)
 #ifdef windows          trgradgp[j][theta]=gradgp[theta][j];
   /* chdir(pathcd);*/    
 #endif  
  /*system("wgnuplot graph.plt");*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
  /*system("../gp37mgw/wgnuplot graph.plt");*/      for(i=1;i<=nlstate;i++)
  /*system("cd ../gp37mgw");*/        for(j=1;j<=nlstate;j++)
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/          vareij[i][j][(int)age] =0.;
  strcpy(plotcmd,GNUPLOTPROGRAM);  
  strcat(plotcmd," ");      for(h=0;h<=nhstepm;h++){
  strcat(plotcmd,optionfilegnuplot);        for(k=0;k<=nhstepm;k++){
  system(plotcmd);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 #ifdef windows          for(i=1;i<=nlstate;i++)
   while (z[0] != 'q') {            for(j=1;j<=nlstate;j++)
     /* chdir(path); */              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");        }
     scanf("%s",z);      }
     if (z[0] == 'c') system("./imach");    
     else if (z[0] == 'e') system(optionfilehtm);      /* pptj */
     else if (z[0] == 'g') system(plotcmd);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     else if (z[0] == 'q') exit(0);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   }      for(j=nlstate+1;j<=nlstate+ndeath;j++)
 #endif        for(i=nlstate+1;i<=nlstate+ndeath;i++)
 }          varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  k1, l1, tj;
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } */ /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else        fprintf(ficgp," %%*lf (%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
   
   #if defined __INTEL_COMPILER
   #if defined(__GNUC__)
           struct utsname sysInfo;  /* For Intel on Linux and OS/X */
   #endif
   #elif defined(__GNUC__) 
   #ifndef  __APPLE__
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
      struct utsname sysInfo;
      int cross = CROSS;
      if (cross){
              printf("Cross-");
              fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
      printf("Compiled with:");fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for ");fprintf(ficlog," for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     double ftolpl = 1.e-10;
     double age, agebase, agelim;
   
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
       agebase=ageminpar;
       agelim=agemaxpar;
   
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           fprintf(ficrespl,"#Age ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
           fprintf(ficrespl,"\n");
           
           for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
   }
   
   int hPijx(double *p, int bage, int fage){
       /*------------- h Pij x at various ages ------------*/
   
     int stepsize;
     int agelim;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
   
     double agedeb;
     double ***p3mat;
   
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       i1= pow(2,cptcoveff);
      for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         /*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
           k=k+1; 
       /* for (k=1; k <= (int) pow(2,cptcoveff); k++){*/
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
               fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         /*}*/
       }
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo();
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
       /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar);
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.46  
changed lines
  Added in v.1.180


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