Diff for /imach/src/imach.c between versions 1.22 and 1.176

version 1.22, 2002/02/22 17:54:20 version 1.176, 2015/01/03 16:45:04
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolate Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.176  2015/01/03 16:45:04  brouard
      *** empty log message ***
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.175  2015/01/03 16:33:42  brouard
   first survey ("cross") where individuals from different ages are    *** empty log message ***
   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 1.174  2015/01/03 16:15:49  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: Still in cross-compilation
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.173  2015/01/03 12:06:26  brouard
   model. More health states you consider, more time is necessary to reach the    Summary: trying to detect cross-compilation
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.172  2014/12/27 12:07:47  brouard
   probabibility to be observed in state j at the second wave    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   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 1.171  2014/12/23 13:26:59  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    Summary: Back from Visual C
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Still problem with utsname.h on Windows
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.170  2014/12/23 11:17:12  brouard
     Summary: Cleaning some \%% back to %%
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    The escape was mandatory for a specific compiler (which one?), but too many warnings.
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.169  2014/12/22 23:08:31  brouard
   account using an interpolation or extrapolation.      Summary: 0.98p
   
   hPijx is the probability to be observed in state i at age x+h    Outputs some informations on compiler used, OS etc. Testing on different platforms.
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.168  2014/12/22 15:17:42  brouard
   states. This elementary transition (by month or quarter trimester,    Summary: update
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.167  2014/12/22 13:50:56  brouard
   and the contribution of each individual to the likelihood is simply    Summary: Testing uname and compiler version and if compiled 32 or 64
   hPijx.  
     Testing on Linux 64
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.166  2014/12/22 11:40:47  brouard
      *** empty log message ***
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.165  2014/12/16 11:20:36  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: After compiling on Visual C
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    * imach.c (Module): Merging 1.61 to 1.162
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.164  2014/12/16 10:52:11  brouard
   **********************************************************************/    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
    
 #include <math.h>    * imach.c (Module): Merging 1.61 to 1.162
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.163  2014/12/16 10:30:11  brouard
 #include <unistd.h>    * imach.c (Module): Merging 1.61 to 1.162
   
 #define MAXLINE 256    Revision 1.162  2014/09/25 11:43:39  brouard
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Summary: temporary backup 0.99!
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.1  2014/09/16 11:06:58  brouard
 #define windows    Summary: With some code (wrong) for nlopt
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Author:
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.161  2014/09/15 20:41:41  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Summary: Problem with macro SQR on Intel compiler
   
 #define NINTERVMAX 8    Revision 1.160  2014/09/02 09:24:05  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    *** empty log message ***
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.159  2014/09/01 10:34:10  brouard
 #define MAXN 20000    Summary: WIN32
 #define YEARM 12. /* Number of months per year */    Author: Brouard
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.158  2014/08/27 17:11:51  brouard
     *** empty log message ***
   
 int erreur; /* Error number */    Revision 1.157  2014/08/27 16:26:55  brouard
 int nvar;    Summary: Preparing windows Visual studio version
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Author: Brouard
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    In order to compile on Visual studio, time.h is now correct and time_t
 int ndeath=1; /* Number of dead states */    and tm struct should be used. difftime should be used but sometimes I
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    just make the differences in raw time format (time(&now).
 int popbased=0;    Trying to suppress #ifdef LINUX
     Add xdg-open for __linux in order to open default browser.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.156  2014/08/25 20:10:10  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    *** empty log message ***
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.155  2014/08/25 18:32:34  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Summary: New compile, minor changes
 double jmean; /* Mean space between 2 waves */    Author: Brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.154  2014/06/20 17:32:08  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    Summary: Outputs now all graphs of convergence to period prevalence
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.153  2014/06/20 16:45:46  brouard
   char filerese[FILENAMELENGTH];    Summary: If 3 live state, convergence to period prevalence on same graph
  FILE  *ficresvij;    Author: Brouard
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.152  2014/06/18 17:54:09  brouard
   char fileresvpl[FILENAMELENGTH];    Summary: open browser, use gnuplot on same dir than imach if not found in the path
   
 #define NR_END 1    Revision 1.151  2014/06/18 16:43:30  brouard
 #define FREE_ARG char*    *** empty log message ***
 #define FTOL 1.0e-10  
     Revision 1.150  2014/06/18 16:42:35  brouard
 #define NRANSI    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 #define ITMAX 200    Author: brouard
   
 #define TOL 2.0e-4    Revision 1.149  2014/06/18 15:51:14  brouard
     Summary: Some fixes in parameter files errors
 #define CGOLD 0.3819660    Author: Nicolas Brouard
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.148  2014/06/17 17:38:48  brouard
     Summary: Nothing new
 #define GOLD 1.618034    Author: Brouard
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Just a new packaging for OS/X version 0.98nS
   
 static double maxarg1,maxarg2;    Revision 1.147  2014/06/16 10:33:11  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    *** empty log message ***
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.146  2014/06/16 10:20:28  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Summary: Merge
 #define rint(a) floor(a+0.5)    Author: Brouard
   
 static double sqrarg;    Merge, before building revised version.
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.145  2014/06/10 21:23:15  brouard
     Summary: Debugging with valgrind
 int imx;    Author: Nicolas Brouard
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Lot of changes in order to output the results with some covariates
     After the Edimburgh REVES conference 2014, it seems mandatory to
 int m,nb;    improve the code.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    No more memory valgrind error but a lot has to be done in order to
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    continue the work of splitting the code into subroutines.
 double **pmmij, ***probs, ***mobaverage;    Also, decodemodel has been improved. Tricode is still not
 double dateintmean=0;    optimal. nbcode should be improved. Documentation has been added in
     the source code.
 double *weight;  
 int **s; /* Status */    Revision 1.143  2014/01/26 09:45:38  brouard
 double *agedc, **covar, idx;    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.142  2014/01/26 03:57:36  brouard
 /**************** split *************************/    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.141  2014/01/26 02:42:01  brouard
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.140  2011/09/02 10:37:54  brouard
 #ifdef windows    Summary: times.h is ok with mingw32 now.
    s = strrchr( path, '\\' );           /* find last / */  
 #else    Revision 1.139  2010/06/14 07:50:17  brouard
    s = strrchr( path, '/' );            /* find last / */    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 #endif    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.138  2010/04/30 18:19:40  brouard
       extern char       *getwd( );    *** empty log message ***
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.137  2010/04/29 18:11:38  brouard
 #else    (Module): Checking covariates for more complex models
       extern char       *getcwd( );    than V1+V2. A lot of change to be done. Unstable.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.136  2010/04/26 20:30:53  brouard
 #endif    (Module): merging some libgsl code. Fixing computation
          return( GLOCK_ERROR_GETCWD );    of likelione (using inter/intrapolation if mle = 0) in order to
       }    get same likelihood as if mle=1.
       strcpy( name, path );             /* we've got it */    Some cleaning of code and comments added.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.135  2009/10/29 15:33:14  brouard
       l2 = strlen( s );                 /* length of filename */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.134  2009/10/29 13:18:53  brouard
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.133  2009/07/06 10:21:25  brouard
    l1 = strlen( dirc );                 /* length of directory */    just nforces
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.132  2009/07/06 08:22:05  brouard
 #else    Many tings
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.131  2009/06/20 16:22:47  brouard
    s = strrchr( name, '.' );            /* find last / */    Some dimensions resccaled
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.130  2009/05/26 06:44:34  brouard
    l1= strlen( name);    (Module): Max Covariate is now set to 20 instead of 8. A
    l2= strlen( s)+1;    lot of cleaning with variables initialized to 0. Trying to make
    strncpy( finame, name, l1-l2);    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    Revision 1.129  2007/08/31 13:49:27  lievre
 }    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   
     Revision 1.128  2006/06/30 13:02:05  brouard
 /******************************************/    (Module): Clarifications on computing e.j
   
 void replace(char *s, char*t)    Revision 1.127  2006/04/28 18:11:50  brouard
 {    (Module): Yes the sum of survivors was wrong since
   int i;    imach-114 because nhstepm was no more computed in the age
   int lg=20;    loop. Now we define nhstepma in the age loop.
   i=0;    (Module): In order to speed up (in case of numerous covariates) we
   lg=strlen(t);    compute health expectancies (without variances) in a first step
   for(i=0; i<= lg; i++) {    and then all the health expectancies with variances or standard
     (s[i] = t[i]);    deviation (needs data from the Hessian matrices) which slows the
     if (t[i]== '\\') s[i]='/';    computation.
   }    In the future we should be able to stop the program is only health
 }    expectancies and graph are needed without standard deviations.
   
 int nbocc(char *s, char occ)    Revision 1.126  2006/04/28 17:23:28  brouard
 {    (Module): Yes the sum of survivors was wrong since
   int i,j=0;    imach-114 because nhstepm was no more computed in the age
   int lg=20;    loop. Now we define nhstepma in the age loop.
   i=0;    Version 0.98h
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.125  2006/04/04 15:20:31  lievre
   if  (s[i] == occ ) j++;    Errors in calculation of health expectancies. Age was not initialized.
   }    Forecasting file added.
   return j;  
 }    Revision 1.124  2006/03/22 17:13:53  lievre
     Parameters are printed with %lf instead of %f (more numbers after the comma).
 void cutv(char *u,char *v, char*t, char occ)    The log-likelihood is printed in the log file
 {  
   int i,lg,j,p=0;    Revision 1.123  2006/03/20 10:52:43  brouard
   i=0;    * imach.c (Module): <title> changed, corresponds to .htm file
   for(j=0; j<=strlen(t)-1; j++) {    name. <head> headers where missing.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    * imach.c (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
   lg=strlen(t);    otherwise the weight is truncated).
   for(j=0; j<p; j++) {    Modification of warning when the covariates values are not 0 or
     (u[j] = t[j]);    1.
   }    Version 0.98g
      u[p]='\0';  
     Revision 1.122  2006/03/20 09:45:41  brouard
    for(j=0; j<= lg; j++) {    (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 1.121  2006/03/16 17:45:01  lievre
 {    * imach.c (Module): Comments concerning covariates added
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    * imach.c (Module): refinements in the computation of lli if
   exit(1);    status=-2 in order to have more reliable computation if stepm is
 }    not 1 month. Version 0.98f
 /*********************** vector *******************/  
 double *vector(int nl, int nh)    Revision 1.120  2006/03/16 15:10:38  lievre
 {    (Module): refinements in the computation of lli if
   double *v;    status=-2 in order to have more reliable computation if stepm is
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    not 1 month. Version 0.98f
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.119  2006/03/15 17:42:26  brouard
 }    (Module): Bug if status = -2, the loglikelihood was
     computed as likelihood omitting the logarithm. Version O.98e
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.118  2006/03/14 18:20:07  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
 /************************ivector *******************************/    (Module): Version 0.98d
 int *ivector(long nl,long nh)  
 {    Revision 1.117  2006/03/14 17:16:22  brouard
   int *v;    (Module): varevsij Comments added explaining the second
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    table of variances if popbased=1 .
   if (!v) nrerror("allocation failure in ivector");    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   return v-nl+NR_END;    (Module): Function pstamp added
 }    (Module): Version 0.98d
   
 /******************free ivector **************************/    Revision 1.116  2006/03/06 10:29:27  brouard
 void free_ivector(int *v, long nl, long nh)    (Module): Variance-covariance wrong links and
 {    varian-covariance of ej. is needed (Saito).
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Revision 1.114  2006/02/26 12:57:58  brouard
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    (Module): Some improvements in processing parameter
 {    filename with strsep.
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    Revision 1.113  2006/02/24 14:20:24  brouard
      (Module): Memory leaks checks with valgrind and:
   /* allocate pointers to rows */    datafile was not closed, some imatrix were not freed and on matrix
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    allocation too.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.112  2006/01/30 09:55:26  brouard
   m -= nrl;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
    
      Revision 1.111  2006/01/25 20:38:18  brouard
   /* allocate rows and set pointers to them */    (Module): Lots of cleaning and bugs added (Gompertz)
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    (Module): Comments can be added in data file. Missing date values
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    can be a simple dot '.'.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.110  2006/01/25 00:51:50  brouard
      (Module): Lots of cleaning and bugs added (Gompertz)
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
      Revision 1.109  2006/01/24 19:37:15  brouard
   /* return pointer to array of pointers to rows */    (Module): Comments (lines starting with a #) are allowed in data.
   return m;  
 }    Revision 1.108  2006/01/19 18:05:42  lievre
     Gnuplot problem appeared...
 /****************** free_imatrix *************************/    To be fixed
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    Revision 1.107  2006/01/19 16:20:37  brouard
       long nch,ncl,nrh,nrl;    Test existence of gnuplot in imach path
      /* free an int matrix allocated by imatrix() */  
 {    Revision 1.106  2006/01/19 13:24:36  brouard
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    Some cleaning and links added in html output
   free((FREE_ARG) (m+nrl-NR_END));  
 }    Revision 1.105  2006/01/05 20:23:19  lievre
     *** empty log message ***
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.104  2005/09/30 16:11:43  lievre
 {    (Module): sump fixed, loop imx fixed, and simplifications.
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    (Module): If the status is missing at the last wave but we know
   double **m;    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    contributions to the likelihood is 1 - Prob of dying from last
   if (!m) nrerror("allocation failure 1 in matrix()");    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   m += NR_END;    the healthy state at last known wave). Version is 0.98
   m -= nrl;  
     Revision 1.103  2005/09/30 15:54:49  lievre
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): sump fixed, loop imx fixed, and simplifications.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.102  2004/09/15 17:31:30  brouard
   m[nrl] -= ncl;    Add the possibility to read data file including tab characters.
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.101  2004/09/15 10:38:38  brouard
   return m;    Fix on curr_time
 }  
     Revision 1.100  2004/07/12 18:29:06  brouard
 /*************************free matrix ************************/    Add version for Mac OS X. Just define UNIX in Makefile
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {    Revision 1.99  2004/06/05 08:57:40  brouard
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    *** empty log message ***
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.98  2004/05/16 15:05:56  brouard
     New version 0.97 . First attempt to estimate force of mortality
 /******************* ma3x *******************************/    directly from the data i.e. without the need of knowing the health
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    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
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    other analysis, in order to test if the mortality estimated from the
   double ***m;    cross-longitudinal survey is different from the mortality estimated
     from other sources like vital statistic data.
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    The same imach parameter file can be used but the option for mle should be -3.
   m += NR_END;  
   m -= nrl;    Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    The output is very simple: only an estimate of the intercept and of
   m[nrl] += NR_END;    the slope with 95% confident intervals.
   m[nrl] -= ncl;  
     Current limitations:
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    A) Even if you enter covariates, i.e. with the
     model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    B) There is no computation of Life Expectancy nor Life Table.
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;    Revision 1.97  2004/02/20 13:25:42  lievre
   m[nrl][ncl] -= nll;    Version 0.96d. Population forecasting command line is (temporarily)
   for (j=ncl+1; j<=nch; j++)    suppressed.
     m[nrl][j]=m[nrl][j-1]+nlay;  
      Revision 1.96  2003/07/15 15:38:55  brouard
   for (i=nrl+1; i<=nrh; i++) {    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    rewritten within the same printf. Workaround: many printfs.
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;    Revision 1.95  2003/07/08 07:54:34  brouard
   }    * imach.c (Repository):
   return m;    (Repository): Using imachwizard code to output a more meaningful covariance
 }    matrix (cov(a12,c31) instead of numbers.
   
 /*************************free ma3x ************************/    Revision 1.94  2003/06/27 13:00:02  brouard
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    Just cleaning
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    Revision 1.93  2003/06/25 16:33:55  brouard
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    (Module): On windows (cygwin) function asctime_r doesn't
   free((FREE_ARG)(m+nrl-NR_END));    exist so I changed back to asctime which exists.
 }    (Module): Version 0.96b
   
 /***************** f1dim *************************/    Revision 1.92  2003/06/25 16:30:45  brouard
 extern int ncom;    (Module): On windows (cygwin) function asctime_r doesn't
 extern double *pcom,*xicom;    exist so I changed back to asctime which exists.
 extern double (*nrfunc)(double []);  
      Revision 1.91  2003/06/25 15:30:29  brouard
 double f1dim(double x)    * imach.c (Repository): Duplicated warning errors corrected.
 {    (Repository): Elapsed time after each iteration is now output. It
   int j;    helps to forecast when convergence will be reached. Elapsed time
   double f;    is stamped in powell.  We created a new html file for the graphs
   double *xt;    concerning matrix of covariance. It has extension -cov.htm.
    
   xt=vector(1,ncom);    Revision 1.90  2003/06/24 12:34:15  brouard
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    (Module): Some bugs corrected for windows. Also, when
   f=(*nrfunc)(xt);    mle=-1 a template is output in file "or"mypar.txt with the design
   free_vector(xt,1,ncom);    of the covariance matrix to be input.
   return f;  
 }    Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
 /*****************brent *************************/    mle=-1 a template is output in file "or"mypar.txt with the design
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    of the covariance matrix to be input.
 {  
   int iter;    Revision 1.88  2003/06/23 17:54:56  brouard
   double a,b,d,etemp;    * 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.
   double fu,fv,fw,fx;  
   double ftemp;    Revision 1.87  2003/06/18 12:26:01  brouard
   double p,q,r,tol1,tol2,u,v,w,x,xm;    Version 0.96
   double e=0.0;  
      Revision 1.86  2003/06/17 20:04:08  brouard
   a=(ax < cx ? ax : cx);    (Module): Change position of html and gnuplot routines and added
   b=(ax > cx ? ax : cx);    routine fileappend.
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);    Revision 1.85  2003/06/17 13:12:43  brouard
   for (iter=1;iter<=ITMAX;iter++) {    * imach.c (Repository): Check when date of death was earlier that
     xm=0.5*(a+b);    current date of interview. It may happen when the death was just
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    prior to the death. In this case, dh was negative and likelihood
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    was wrong (infinity). We still send an "Error" but patch by
     printf(".");fflush(stdout);    assuming that the date of death was just one stepm after the
 #ifdef DEBUG    interview.
     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);    (Repository): Because some people have very long ID (first column)
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    we changed int to long in num[] and we added a new lvector for
 #endif    memory allocation. But we also truncated to 8 characters (left
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    truncation)
       *xmin=x;    (Repository): No more line truncation errors.
       return fx;  
     }    Revision 1.84  2003/06/13 21:44:43  brouard
     ftemp=fu;    * imach.c (Repository): Replace "freqsummary" at a correct
     if (fabs(e) > tol1) {    place. It differs from routine "prevalence" which may be called
       r=(x-w)*(fx-fv);    many times. Probs is memory consuming and must be used with
       q=(x-v)*(fx-fw);    parcimony.
       p=(x-v)*q-(x-w)*r;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;    Revision 1.83  2003/06/10 13:39:11  lievre
       q=fabs(q);    *** empty log message ***
       etemp=e;  
       e=d;    Revision 1.82  2003/06/05 15:57:20  brouard
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    Add log in  imach.c and  fullversion number is now printed.
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {  */
         d=p/q;  /*
         u=x+d;     Interpolated Markov Chain
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);    Short summary of the programme:
       }    
     } else {    This program computes Healthy Life Expectancies from
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     }    first survey ("cross") where individuals from different ages are
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    interviewed on their health status or degree of disability (in the
     fu=(*f)(u);    case of a health survey which is our main interest) -2- at least a
     if (fu <= fx) {    second wave of interviews ("longitudinal") which measure each change
       if (u >= x) a=x; else b=x;    (if any) in individual health status.  Health expectancies are
       SHFT(v,w,x,u)    computed from the time spent in each health state according to a
         SHFT(fv,fw,fx,fu)    model. More health states you consider, more time is necessary to reach the
         } else {    Maximum Likelihood of the parameters involved in the model.  The
           if (u < x) a=u; else b=u;    simplest model is the multinomial logistic model where pij is the
           if (fu <= fw || w == x) {    probability to be observed in state j at the second wave
             v=w;    conditional to be observed in state i at the first wave. Therefore
             w=u;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
             fv=fw;    'age' is age and 'sex' is a covariate. If you want to have a more
             fw=fu;    complex model than "constant and age", you should modify the program
           } else if (fu <= fv || v == x || v == w) {    where the markup *Covariates have to be included here again* invites
             v=u;    you to do it.  More covariates you add, slower the
             fv=fu;    convergence.
           }  
         }    The advantage of this computer programme, compared to a simple
   }    multinomial logistic model, is clear when the delay between waves is not
   nrerror("Too many iterations in brent");    identical for each individual. Also, if a individual missed an
   *xmin=x;    intermediate interview, the information is lost, but taken into
   return fx;    account using an interpolation or extrapolation.  
 }  
     hPijx is the probability to be observed in state i at age x+h
 /****************** mnbrak ***********************/    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    states. This elementary transition (by month, quarter,
             double (*func)(double))    semester or year) is modelled as a multinomial logistic.  The hPx
 {    matrix is simply the matrix product of nh*stepm elementary matrices
   double ulim,u,r,q, dum;    and the contribution of each individual to the likelihood is simply
   double fu;    hPijx.
    
   *fa=(*func)(*ax);    Also this programme outputs the covariance matrix of the parameters but also
   *fb=(*func)(*bx);    of the life expectancies. It also computes the period (stable) prevalence. 
   if (*fb > *fa) {    
     SHFT(dum,*ax,*bx,dum)    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
       SHFT(dum,*fb,*fa,dum)             Institut national d'études démographiques, Paris.
       }    This software have been partly granted by Euro-REVES, a concerted action
   *cx=(*bx)+GOLD*(*bx-*ax);    from the European Union.
   *fc=(*func)(*cx);    It is copyrighted identically to a GNU software product, ie programme and
   while (*fb > *fc) {    software can be distributed freely for non commercial use. Latest version
     r=(*bx-*ax)*(*fb-*fc);    can be accessed at http://euroreves.ined.fr/imach .
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     ulim=(*bx)+GLIMIT*(*cx-*bx);    
     if ((*bx-u)*(u-*cx) > 0.0) {    **********************************************************************/
       fu=(*func)(u);  /*
     } else if ((*cx-u)*(u-ulim) > 0.0) {    main
       fu=(*func)(u);    read parameterfile
       if (fu < *fc) {    read datafile
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    concatwav
           SHFT(*fb,*fc,fu,(*func)(u))    freqsummary
           }    if (mle >= 1)
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      mlikeli
       u=ulim;    print results files
       fu=(*func)(u);    if mle==1 
     } else {       computes hessian
       u=(*cx)+GOLD*(*cx-*bx);    read end of parameter file: agemin, agemax, bage, fage, estepm
       fu=(*func)(u);        begin-prev-date,...
     }    open gnuplot file
     SHFT(*ax,*bx,*cx,u)    open html file
       SHFT(*fa,*fb,*fc,fu)    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
       }     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
 }                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
       freexexit2 possible for memory heap.
 /*************** linmin ************************/  
     h Pij x                         | pij_nom  ficrestpij
 int ncom;     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
 double *pcom,*xicom;         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
 double (*nrfunc)(double []);         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
 {         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   double brent(double ax, double bx, double cx,    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
                double (*f)(double), double tol, double *xmin);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   double f1dim(double x);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));    forecasting if prevfcast==1 prevforecast call prevalence()
   int j;    health expectancies
   double xx,xmin,bx,ax;    Variance-covariance of DFLE
   double fx,fb,fa;    prevalence()
       movingaverage()
   ncom=n;    varevsij() 
   pcom=vector(1,n);    if popbased==1 varevsij(,popbased)
   xicom=vector(1,n);    total life expectancies
   nrfunc=func;    Variance of period (stable) prevalence
   for (j=1;j<=n;j++) {   end
     pcom[j]=p[j];  */
     xicom[j]=xi[j];  
   }  #define POWELL /* Instead of NLOPT */
   ax=0.0;  
   xx=1.0;  #include <math.h>
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  #include <stdio.h>
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #include <stdlib.h>
 #ifdef DEBUG  #include <string.h>
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  #ifdef _WIN32
   for (j=1;j<=n;j++) {  #include <io.h>
     xi[j] *= xmin;  #include <windows.h>
     p[j] += xi[j];  #include <tchar.h>
   }  #else
   free_vector(xicom,1,n);  #include <unistd.h>
   free_vector(pcom,1,n);  #endif
 }  
   #include <limits.h>
 /*************** powell ************************/  #include <sys/types.h>
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))  #if defined(__GNUC__)
 {  #include <sys/utsname.h> /* Doesn't work on Windows */
   void linmin(double p[], double xi[], int n, double *fret,  #endif
               double (*func)(double []));  
   int i,ibig,j;  #include <sys/stat.h>
   double del,t,*pt,*ptt,*xit;  #include <errno.h>
   double fp,fptt;  /* extern int errno; */
   double *xits;  
   pt=vector(1,n);  /* #ifdef LINUX */
   ptt=vector(1,n);  /* #include <time.h> */
   xit=vector(1,n);  /* #include "timeval.h" */
   xits=vector(1,n);  /* #else */
   *fret=(*func)(p);  /* #include <sys/time.h> */
   for (j=1;j<=n;j++) pt[j]=p[j];  /* #endif */
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);  #include <time.h>
     ibig=0;  
     del=0.0;  #ifdef GSL
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #include <gsl/gsl_errno.h>
     for (i=1;i<=n;i++)  #include <gsl/gsl_multimin.h>
       printf(" %d %.12f",i, p[i]);  #endif
     printf("\n");  
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  #ifdef NLOPT
       fptt=(*fret);  #include <nlopt.h>
 #ifdef DEBUG  typedef struct {
       printf("fret=%lf \n",*fret);    double (* function)(double [] );
 #endif  } myfunc_data ;
       printf("%d",i);fflush(stdout);  #endif
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  /* #include <libintl.h> */
         del=fabs(fptt-(*fret));  /* #define _(String) gettext (String) */
         ibig=i;  
       }  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  #define GNUPLOTPROGRAM "gnuplot"
       for (j=1;j<=n;j++) {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #define FILENAMELENGTH 132
         printf(" x(%d)=%.12e",j,xit[j]);  
       }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       for(j=1;j<=n;j++)  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
         printf(" p=%.12e",p[j]);  
       printf("\n");  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
 #endif  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #define NINTERVMAX 8
 #ifdef DEBUG  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
       int k[2],l;  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
       k[0]=1;  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
       k[1]=-1;  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
       printf("Max: %.12e",(*func)(p));  #define MAXN 20000
       for (j=1;j<=n;j++)  #define YEARM 12. /**< Number of months per year */
         printf(" %.12e",p[j]);  #define AGESUP 130
       printf("\n");  #define AGEBASE 40
       for(l=0;l<=1;l++) {  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
         for (j=1;j<=n;j++) {  #ifdef _WIN32
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  #define DIRSEPARATOR '\\'
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  #define CHARSEPARATOR "\\"
         }  #define ODIRSEPARATOR '/'
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  #else
       }  #define DIRSEPARATOR '/'
 #endif  #define CHARSEPARATOR "/"
   #define ODIRSEPARATOR '\\'
   #endif
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  /* $Id$ */
       free_vector(ptt,1,n);  /* $State$ */
       free_vector(pt,1,n);  
       return;  char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
     }  char fullversion[]="$Revision$ $Date$"; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  char strstart[80];
     for (j=1;j<=n;j++) {  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       ptt[j]=2.0*p[j]-pt[j];  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
       xit[j]=p[j]-pt[j];  int nvar=0, nforce=0; /* Number of variables, number of forces */
       pt[j]=p[j];  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
     }  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
     fptt=(*func)(ptt);  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
     if (fptt < fp) {  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
       if (t < 0.0) {  int cptcovprodnoage=0; /**< Number of covariate products without age */   
         linmin(p,xit,n,fret,func);  int cptcoveff=0; /* Total number of covariates to vary for printing results */
         for (j=1;j<=n;j++) {  int cptcov=0; /* Working variable */
           xi[j][ibig]=xi[j][n];  int npar=NPARMAX;
           xi[j][n]=xit[j];  int nlstate=2; /* Number of live states */
         }  int ndeath=1; /* Number of dead states */
 #ifdef DEBUG  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int popbased=0;
         for(j=1;j<=n;j++)  
           printf(" %.12e",xit[j]);  int *wav; /* Number of waves for this individuual 0 is possible */
         printf("\n");  int maxwav=0; /* Maxim number of waves */
 #endif  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
       }  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     }  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   }                     to the likelihood and the sum of weights (done by funcone)*/
 }  int mle=1, weightopt=0;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 /**** Prevalence limit ****************/  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 {  int countcallfunc=0;  /* Count the number of calls to func */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  double jmean=1; /* Mean space between 2 waves */
      matrix by transitions matrix until convergence is reached */  double **matprod2(); /* test */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
   int i, ii,j,k;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   double min, max, maxmin, maxmax,sumnew=0.;  /*FILE *fic ; */ /* Used in readdata only */
   double **matprod2();  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   double **out, cov[NCOVMAX], **pmij();  FILE *ficlog, *ficrespow;
   double **newm;  int globpr=0; /* Global variable for printing or not */
   double agefin, delaymax=50 ; /* Max number of years to converge */  double fretone; /* Only one call to likelihood */
   long ipmx=0; /* Number of contributions */
   for (ii=1;ii<=nlstate+ndeath;ii++)  double sw; /* Sum of weights */
     for (j=1;j<=nlstate+ndeath;j++){  char filerespow[FILENAMELENGTH];
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
     }  FILE *ficresilk;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
    cov[1]=1.;  FILE *ficresprobmorprev;
    FILE *fichtm, *fichtmcov; /* Html File */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  FILE *ficreseij;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  char filerese[FILENAMELENGTH];
     newm=savm;  FILE *ficresstdeij;
     /* Covariates have to be included here again */  char fileresstde[FILENAMELENGTH];
      cov[2]=agefin;  FILE *ficrescveij;
    char filerescve[FILENAMELENGTH];
       for (k=1; k<=cptcovn;k++) {  FILE  *ficresvij;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  char fileresv[FILENAMELENGTH];
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  FILE  *ficresvpl;
       }  char fileresvpl[FILENAMELENGTH];
       for (k=1; k<=cptcovage;k++)  char title[MAXLINE];
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       for (k=1; k<=cptcovprod;k++)  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   char command[FILENAMELENGTH];
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  int  outcmd=0;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
   char filelog[FILENAMELENGTH]; /* Log file */
     savm=oldm;  char filerest[FILENAMELENGTH];
     oldm=newm;  char fileregp[FILENAMELENGTH];
     maxmax=0.;  char popfile[FILENAMELENGTH];
     for(j=1;j<=nlstate;j++){  
       min=1.;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       max=0.;  
       for(i=1; i<=nlstate; i++) {  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
         sumnew=0;  /* struct timezone tzp; */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  /* extern int gettimeofday(); */
         prlim[i][j]= newm[i][j]/(1-sumnew);  struct tm tml, *gmtime(), *localtime();
         max=FMAX(max,prlim[i][j]);  
         min=FMIN(min,prlim[i][j]);  extern time_t time();
       }  
       maxmin=max-min;  struct tm start_time, end_time, curr_time, last_time, forecast_time;
       maxmax=FMAX(maxmax,maxmin);  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
     }  struct tm tm;
     if(maxmax < ftolpl){  
       return prlim;  char strcurr[80], strfor[80];
     }  
   }  char *endptr;
 }  long lval;
   double dval;
 /*************** transition probabilities ***************/  
   #define NR_END 1
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  #define FREE_ARG char*
 {  #define FTOL 1.0e-10
   double s1, s2;  
   /*double t34;*/  #define NRANSI 
   int i,j,j1, nc, ii, jj;  #define ITMAX 200 
   
     for(i=1; i<= nlstate; i++){  #define TOL 2.0e-4 
     for(j=1; j<i;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #define CGOLD 0.3819660 
         /*s2 += param[i][j][nc]*cov[nc];*/  #define ZEPS 1.0e-10 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  #define GOLD 1.618034 
       ps[i][j]=s2;  #define GLIMIT 100.0 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  #define TINY 1.0e-20 
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){  static double maxarg1,maxarg2;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    
       }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       ps[i][j]=s2;  #define rint(a) floor(a+0.5)
     }  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
   }  /* #define mytinydouble 1.0e-16 */
     /*ps[3][2]=1;*/  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
   /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   for(i=1; i<= nlstate; i++){  /* static double dsqrarg; */
      s1=0;  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
     for(j=1; j<i; j++)  static double sqrarg;
       s1+=exp(ps[i][j]);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     for(j=i+1; j<=nlstate+ndeath; j++)  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       s1+=exp(ps[i][j]);  int agegomp= AGEGOMP;
     ps[i][i]=1./(s1+1.);  
     for(j=1; j<i; j++)  int imx; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  int stepm=1;
     for(j=i+1; j<=nlstate+ndeath; j++)  /* Stepm, step in month: minimum step interpolation*/
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  int estepm;
   } /* end i */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  int m,nb;
     for(jj=1; jj<= nlstate+ndeath; jj++){  long *num;
       ps[ii][jj]=0;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       ps[ii][ii]=1;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     }  double **pmmij, ***probs;
   }  double *ageexmed,*agecens;
   double dateintmean=0;
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  double *weight;
     for(jj=1; jj<= nlstate+ndeath; jj++){  int **s; /* Status */
      printf("%lf ",ps[ii][jj]);  double *agedc;
    }  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
     printf("\n ");                    * covar=matrix(0,NCOVMAX,1,n); 
     }                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
     printf("\n ");printf("%lf ",cov[2]);*/  double  idx; 
 /*  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  int *Ndum; /** Freq of modality (tricode */
   goto end;*/  int **codtab; /**< codtab=imatrix(1,100,1,10); */
     return ps;  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
 }  double *lsurv, *lpop, *tpop;
   
 /**************** Product of 2 matrices ******************/  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   double ftolhess; /**< Tolerance for computing hessian */
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  
 {  /**************** split *************************/
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  {
   /* in, b, out are matrice of pointers which should have been initialized    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
      before: only the contents of out is modified. The function returns       the name of the file (name), its extension only (ext) and its first part of the name (finame)
      a pointer to pointers identical to out */    */ 
   long i, j, k;    char  *ss;                            /* pointer */
   for(i=nrl; i<= nrh; i++)    int   l1, l2;                         /* length counters */
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    l1 = strlen(path );                   /* length of path */
         out[i][k] +=in[i][j]*b[j][k];    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   return out;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
 }      strcpy( name, path );               /* we got the fullname name because no directory */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 /************* Higher Matrix Product ***************/      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 {        return( GLOCK_ERROR_GETCWD );
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      }
      duration (i.e. until      /* got dirc from getcwd*/
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      printf(" DIRC = %s \n",dirc);
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    } else {                              /* strip direcotry from path */
      (typically every 2 years instead of every month which is too big).      ss++;                               /* after this, the filename */
      Model is determined by parameters x and covariates have to be      l2 = strlen( ss );                  /* length of filename */
      included manually here.      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
      */      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
   int i, j, d, h, k;      printf(" DIRC2 = %s \n",dirc);
   double **out, cov[NCOVMAX];    }
   double **newm;    /* We add a separator at the end of dirc if not exists */
     l1 = strlen( dirc );                  /* length of directory */
   /* Hstepm could be zero and should return the unit matrix */    if( dirc[l1-1] != DIRSEPARATOR ){
   for (i=1;i<=nlstate+ndeath;i++)      dirc[l1] =  DIRSEPARATOR;
     for (j=1;j<=nlstate+ndeath;j++){      dirc[l1+1] = 0; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      printf(" DIRC3 = %s \n",dirc);
       po[i][j][0]=(i==j ? 1.0 : 0.0);    }
     }    ss = strrchr( name, '.' );            /* find last / */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    if (ss >0){
   for(h=1; h <=nhstepm; h++){      ss++;
     for(d=1; d <=hstepm; d++){      strcpy(ext,ss);                     /* save extension */
       newm=savm;      l1= strlen( name);
       /* Covariates have to be included here again */      l2= strlen(ss)+1;
       cov[1]=1.;      strncpy( finame, name, l1-l2);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      finame[l1-l2]= 0;
       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];    return( 0 );                          /* we're done */
       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]]];  
   
   /******************************************/
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  void replace_back_to_slash(char *s, char*t)
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  {
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    int i;
       savm=oldm;    int lg=0;
       oldm=newm;    i=0;
     }    lg=strlen(t);
     for(i=1; i<=nlstate+ndeath; i++)    for(i=0; i<= lg; i++) {
       for(j=1;j<=nlstate+ndeath;j++) {      (s[i] = t[i]);
         po[i][j][h]=newm[i][j];      if (t[i]== '\\') s[i]='/';
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    }
          */  }
       }  
   } /* end h */  char *trimbb(char *out, char *in)
   return po;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
 }    char *s;
     s=out;
     while (*in != '\0'){
 /*************** log-likelihood *************/      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
 double func( double *x)        in++;
 {      }
   int i, ii, j, k, mi, d, kk;      *out++ = *in++;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    }
   double **out;    *out='\0';
   double sw; /* Sum of weights */    return s;
   double lli; /* Individual log likelihood */  }
   long ipmx;  
   /*extern weight */  char *cutl(char *blocc, char *alocc, char *in, char occ)
   /* We are differentiating ll according to initial status */  {
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
   /*for(i=1;i<imx;i++)       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     printf(" %d\n",s[4][i]);       gives blocc="abcdef2ghi" and alocc="j".
   */       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   cov[1]=1.;    */
     char *s, *t;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    t=in;s=in;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    while ((*in != occ) && (*in != '\0')){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      *alocc++ = *in++;
     for(mi=1; mi<= wav[i]-1; mi++){    }
       for (ii=1;ii<=nlstate+ndeath;ii++)    if( *in == occ){
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      *(alocc)='\0';
       for(d=0; d<dh[mi][i]; d++){      s=++in;
         newm=savm;    }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;   
         for (kk=1; kk<=cptcovage;kk++) {    if (s == t) {/* occ not found */
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      *(alocc-(in-s))='\0';
         }      in=s;
            }
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    while ( *in != '\0'){
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      *blocc++ = *in++;
         savm=oldm;    }
         oldm=newm;  
            *blocc='\0';
            return t;
       } /* end mult */  }
        char *cutv(char *blocc, char *alocc, char *in, char occ)
       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]]);*/    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
       ipmx +=1;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       sw += weight[i];       gives blocc="abcdef2ghi" and alocc="j".
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     } /* end of wave */    */
   } /* end of individual */    char *s, *t;
     t=in;s=in;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    while (*in != '\0'){
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      while( *in == occ){
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        *blocc++ = *in++;
   return -l;        s=in;
 }      }
       *blocc++ = *in++;
     }
 /*********** Maximum Likelihood Estimation ***************/    if (s == t) /* occ not found */
       *(blocc-(in-s))='\0';
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    else
 {      *(blocc-(in-s)-1)='\0';
   int i,j, iter;    in=s;
   double **xi,*delti;    while ( *in != '\0'){
   double fret;      *alocc++ = *in++;
   xi=matrix(1,npar,1,npar);    }
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)    *alocc='\0';
       xi[i][j]=(i==j ? 1.0 : 0.0);    return s;
   printf("Powell\n");  }
   powell(p,xi,npar,ftol,&iter,&fret,func);  
   int nbocc(char *s, char occ)
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  {
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    int i,j=0;
     int lg=20;
 }    i=0;
     lg=strlen(s);
 /**** Computes Hessian and covariance matrix ***/    for(i=0; i<= lg; i++) {
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    if  (s[i] == occ ) j++;
 {    }
   double  **a,**y,*x,pd;    return j;
   double **hess;  }
   int i, j,jk;  
   int *indx;  /* void cutv(char *u,char *v, char*t, char occ) */
   /* { */
   double hessii(double p[], double delta, int theta, double delti[]);  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   double hessij(double p[], double delti[], int i, int j);  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   void lubksb(double **a, int npar, int *indx, double b[]) ;  /*      gives u="abcdef2ghi" and v="j" *\/ */
   void ludcmp(double **a, int npar, int *indx, double *d) ;  /*   int i,lg,j,p=0; */
   /*   i=0; */
   hess=matrix(1,npar,1,npar);  /*   lg=strlen(t); */
   /*   for(j=0; j<=lg-1; j++) { */
   printf("\nCalculation of the hessian matrix. Wait...\n");  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   for (i=1;i<=npar;i++){  /*   } */
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);  /*   for(j=0; j<p; j++) { */
     /*printf(" %f ",p[i]);*/  /*     (u[j] = t[j]); */
     /*printf(" %lf ",hess[i][i]);*/  /*   } */
   }  /*      u[p]='\0'; */
    
   for (i=1;i<=npar;i++) {  /*    for(j=0; j<= lg; j++) { */
     for (j=1;j<=npar;j++)  {  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
       if (j>i) {  /*   } */
         printf(".%d%d",i,j);fflush(stdout);  /* } */
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];      #ifdef _WIN32
         /*printf(" %lf ",hess[i][j]);*/  char * strsep(char **pp, const char *delim)
       }  {
     }    char *p, *q;
   }           
   printf("\n");    if ((p = *pp) == NULL)
       return 0;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    if ((q = strpbrk (p, delim)) != NULL)
      {
   a=matrix(1,npar,1,npar);      *pp = q + 1;
   y=matrix(1,npar,1,npar);      *q = '\0';
   x=vector(1,npar);    }
   indx=ivector(1,npar);    else
   for (i=1;i<=npar;i++)      *pp = 0;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    return p;
   ludcmp(a,npar,indx,&pd);  }
   #endif
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  /********************** nrerror ********************/
     x[j]=1;  
     lubksb(a,npar,indx,x);  void nrerror(char error_text[])
     for (i=1;i<=npar;i++){  {
       matcov[i][j]=x[i];    fprintf(stderr,"ERREUR ...\n");
     }    fprintf(stderr,"%s\n",error_text);
   }    exit(EXIT_FAILURE);
   }
   printf("\n#Hessian matrix#\n");  /*********************** vector *******************/
   for (i=1;i<=npar;i++) {  double *vector(int nl, int nh)
     for (j=1;j<=npar;j++) {  {
       printf("%.3e ",hess[i][j]);    double *v;
     }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     printf("\n");    if (!v) nrerror("allocation failure in vector");
   }    return v-nl+NR_END;
   }
   /* Recompute Inverse */  
   for (i=1;i<=npar;i++)  /************************ free vector ******************/
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  void free_vector(double*v, int nl, int nh)
   ludcmp(a,npar,indx,&pd);  {
     free((FREE_ARG)(v+nl-NR_END));
   /*  printf("\n#Hessian matrix recomputed#\n");  }
   
   for (j=1;j<=npar;j++) {  /************************ivector *******************************/
     for (i=1;i<=npar;i++) x[i]=0;  int *ivector(long nl,long nh)
     x[j]=1;  {
     lubksb(a,npar,indx,x);    int *v;
     for (i=1;i<=npar;i++){    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       y[i][j]=x[i];    if (!v) nrerror("allocation failure in ivector");
       printf("%.3e ",y[i][j]);    return v-nl+NR_END;
     }  }
     printf("\n");  
   }  /******************free ivector **************************/
   */  void free_ivector(int *v, long nl, long nh)
   {
   free_matrix(a,1,npar,1,npar);    free((FREE_ARG)(v+nl-NR_END));
   free_matrix(y,1,npar,1,npar);  }
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);  /************************lvector *******************************/
   free_matrix(hess,1,npar,1,npar);  long *lvector(long nl,long nh)
   {
     long *v;
 }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     if (!v) nrerror("allocation failure in ivector");
 /*************** hessian matrix ****************/    return v-nl+NR_END;
 double hessii( double x[], double delta, int theta, double delti[])  }
 {  
   int i;  /******************free lvector **************************/
   int l=1, lmax=20;  void free_lvector(long *v, long nl, long nh)
   double k1,k2;  {
   double p2[NPARMAX+1];    free((FREE_ARG)(v+nl-NR_END));
   double res;  }
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  
   double fx;  /******************* imatrix *******************************/
   int k=0,kmax=10;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   double l1;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   { 
   fx=func(x);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   for (i=1;i<=npar;i++) p2[i]=x[i];    int **m; 
   for(l=0 ; l <=lmax; l++){    
     l1=pow(10,l);    /* allocate pointers to rows */ 
     delts=delt;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     for(k=1 ; k <kmax; k=k+1){    if (!m) nrerror("allocation failure 1 in matrix()"); 
       delt = delta*(l1*k);    m += NR_END; 
       p2[theta]=x[theta] +delt;    m -= nrl; 
       k1=func(p2)-fx;    
       p2[theta]=x[theta]-delt;    
       k2=func(p2)-fx;    /* allocate rows and set pointers to them */ 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
          m[nrl] += NR_END; 
 #ifdef DEBUG    m[nrl] -= ncl; 
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    
 #endif    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    /* return pointer to array of pointers to rows */ 
         k=kmax;    return m; 
       }  } 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  
         k=kmax; l=lmax*10.;  /****************** free_imatrix *************************/
       }  void free_imatrix(m,nrl,nrh,ncl,nch)
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        int **m;
         delts=delt;        long nch,ncl,nrh,nrl; 
       }       /* free an int matrix allocated by imatrix() */ 
     }  { 
   }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   delti[theta]=delts;    free((FREE_ARG) (m+nrl-NR_END)); 
   return res;  } 
    
 }  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
 double hessij( double x[], double delti[], int thetai,int thetaj)  {
 {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   int i;    double **m;
   int l=1, l1, lmax=20;  
   double k1,k2,k3,k4,res,fx;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double p2[NPARMAX+1];    if (!m) nrerror("allocation failure 1 in matrix()");
   int k;    m += NR_END;
     m -= nrl;
   fx=func(x);  
   for (k=1; k<=2; k++) {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     for (i=1;i<=npar;i++) p2[i]=x[i];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     p2[thetai]=x[thetai]+delti[thetai]/k;    m[nrl] += NR_END;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    m[nrl] -= ncl;
     k1=func(p2)-fx;  
      for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     p2[thetai]=x[thetai]+delti[thetai]/k;    return m;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     k2=func(p2)-fx;  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
    that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     p2[thetai]=x[thetai]-delti[thetai]/k;     */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  }
     k3=func(p2)-fx;  
    /*************************free matrix ************************/
     p2[thetai]=x[thetai]-delti[thetai]/k;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  {
     k4=func(p2)-fx;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    free((FREE_ARG)(m+nrl-NR_END));
 #ifdef DEBUG  }
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  
 #endif  /******************* ma3x *******************************/
   }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   return res;  {
 }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 {    if (!m) nrerror("allocation failure 1 in matrix()");
   int i,imax,j,k;    m += NR_END;
   double big,dum,sum,temp;    m -= nrl;
   double *vv;  
      m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   vv=vector(1,n);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   *d=1.0;    m[nrl] += NR_END;
   for (i=1;i<=n;i++) {    m[nrl] -= ncl;
     big=0.0;  
     for (j=1;j<=n;j++)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     vv[i]=1.0/big;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   }    m[nrl][ncl] += NR_END;
   for (j=1;j<=n;j++) {    m[nrl][ncl] -= nll;
     for (i=1;i<j;i++) {    for (j=ncl+1; j<=nch; j++) 
       sum=a[i][j];      m[nrl][j]=m[nrl][j-1]+nlay;
       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][ncl]=m[i-1l][ncl]+ncol*nlay;
     big=0.0;      for (j=ncl+1; j<=nch; j++) 
     for (i=j;i<=n;i++) {        m[i][j]=m[i][j-1]+nlay;
       sum=a[i][j];    }
       for (k=1;k<j;k++)    return m; 
         sum -= a[i][k]*a[k][j];    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       a[i][j]=sum;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       if ( (dum=vv[i]*fabs(sum)) >= big) {    */
         big=dum;  }
         imax=i;  
       }  /*************************free ma3x ************************/
     }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     if (j != imax) {  {
       for (k=1;k<=n;k++) {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         dum=a[imax][k];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         a[imax][k]=a[j][k];    free((FREE_ARG)(m+nrl-NR_END));
         a[j][k]=dum;  }
       }  
       *d = -(*d);  /*************** function subdirf ***********/
       vv[imax]=vv[j];  char *subdirf(char fileres[])
     }  {
     indx[j]=imax;    /* Caution optionfilefiname is hidden */
     if (a[j][j] == 0.0) a[j][j]=TINY;    strcpy(tmpout,optionfilefiname);
     if (j != n) {    strcat(tmpout,"/"); /* Add to the right */
       dum=1.0/(a[j][j]);    strcat(tmpout,fileres);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    return tmpout;
     }  }
   }  
   free_vector(vv,1,n);  /* Doesn't work */  /*************** function subdirf2 ***********/
 ;  char *subdirf2(char fileres[], char *preop)
 }  {
     
 void lubksb(double **a, int n, int *indx, double b[])    /* Caution optionfilefiname is hidden */
 {    strcpy(tmpout,optionfilefiname);
   int i,ii=0,ip,j;    strcat(tmpout,"/");
   double sum;    strcat(tmpout,preop);
      strcat(tmpout,fileres);
   for (i=1;i<=n;i++) {    return tmpout;
     ip=indx[i];  }
     sum=b[ip];  
     b[ip]=b[i];  /*************** function subdirf3 ***********/
     if (ii)  char *subdirf3(char fileres[], char *preop, char *preop2)
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  {
     else if (sum) ii=i;    
     b[i]=sum;    /* Caution optionfilefiname is hidden */
   }    strcpy(tmpout,optionfilefiname);
   for (i=n;i>=1;i--) {    strcat(tmpout,"/");
     sum=b[i];    strcat(tmpout,preop);
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    strcat(tmpout,preop2);
     b[i]=sum/a[i][i];    strcat(tmpout,fileres);
   }    return tmpout;
 }  }
   
 /************ Frequencies ********************/  char *asc_diff_time(long time_sec, char ascdiff[])
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)  {
 {  /* Some frequencies */    long sec_left, days, hours, minutes;
      days = (time_sec) / (60*60*24);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    sec_left = (time_sec) % (60*60*24);
   double ***freq; /* Frequencies */    hours = (sec_left) / (60*60) ;
   double *pp;    sec_left = (sec_left) %(60*60);
   double pos, k2, dateintsum=0,k2cpt=0;    minutes = (sec_left) /60;
   FILE *ficresp;    sec_left = (sec_left) % (60);
   char fileresp[FILENAMELENGTH];    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
   pp=vector(1,nlstate);  }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   strcpy(fileresp,"p");  /***************** f1dim *************************/
   strcat(fileresp,fileres);  extern int ncom; 
   if((ficresp=fopen(fileresp,"w"))==NULL) {  extern double *pcom,*xicom;
     printf("Problem with prevalence resultfile: %s\n", fileresp);  extern double (*nrfunc)(double []); 
     exit(0);   
   }  double f1dim(double x) 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  { 
   j1=0;    int j; 
     double f;
   j=cptcoveff;    double *xt; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}   
     xt=vector(1,ncom); 
   for(k1=1; k1<=j;k1++){    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
    for(i1=1; i1<=ncodemax[k1];i1++){    f=(*nrfunc)(xt); 
        j1++;    free_vector(xt,1,ncom); 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    return f; 
          scanf("%d", i);*/  } 
         for (i=-1; i<=nlstate+ndeath; i++)    
          for (jk=-1; jk<=nlstate+ndeath; jk++)    /*****************brent *************************/
            for(m=agemin; m <= agemax+3; m++)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
              freq[i][jk][m]=0;  { 
     int iter; 
         dateintsum=0;    double a,b,d,etemp;
         k2cpt=0;    double fu=0,fv,fw,fx;
        for (i=1; i<=imx; i++) {    double ftemp=0.;
          bool=1;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
          if  (cptcovn>0) {    double e=0.0; 
            for (z1=1; z1<=cptcoveff; z1++)   
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    a=(ax < cx ? ax : cx); 
                bool=0;    b=(ax > cx ? ax : cx); 
          }    x=w=v=bx; 
          if (bool==1) {    fw=fv=fx=(*f)(x); 
            for(m=firstpass; m<=lastpass; m++){    for (iter=1;iter<=ITMAX;iter++) { 
              k2=anint[m][i]+(mint[m][i]/12.);      xm=0.5*(a+b); 
              if ((k2>=dateprev1) && (k2<=dateprev2)) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
                if(agev[m][i]==0) agev[m][i]=agemax+1;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
                if(agev[m][i]==1) agev[m][i]=agemax+2;      printf(".");fflush(stdout);
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      fprintf(ficlog,".");fflush(ficlog);
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  #ifdef DEBUGBRENT
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      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);
                  dateintsum=dateintsum+k2;      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);
                  k2cpt++;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
                }  #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
              }        *xmin=x; 
            }        return fx; 
          }      } 
        }      ftemp=fu;
         if  (cptcovn>0) {      if (fabs(e) > tol1) { 
          fprintf(ficresp, "\n#********** Variable ");        r=(x-w)*(fx-fv); 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        q=(x-v)*(fx-fw); 
        fprintf(ficresp, "**********\n#");        p=(x-v)*q-(x-w)*r; 
         }        q=2.0*(q-r); 
        for(i=1; i<=nlstate;i++)        if (q > 0.0) p = -p; 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        q=fabs(q); 
        fprintf(ficresp, "\n");        etemp=e; 
                e=d; 
   for(i=(int)agemin; i <= (int)agemax+3; i++){        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     if(i==(int)agemax+3)          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       printf("Total");        else { 
     else          d=p/q; 
       printf("Age %d", i);          u=x+d; 
     for(jk=1; jk <=nlstate ; jk++){          if (u-a < tol2 || b-u < tol2) 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            d=SIGN(tol1,xm-x); 
         pp[jk] += freq[jk][m][i];        } 
     }      } else { 
     for(jk=1; jk <=nlstate ; jk++){        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for(m=-1, pos=0; m <=0 ; m++)      } 
         pos += freq[jk][m][i];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       if(pp[jk]>=1.e-10)      fu=(*f)(u); 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      if (fu <= fx) { 
       else        if (u >= x) a=x; else b=x; 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        SHFT(v,w,x,u) 
     }          SHFT(fv,fw,fx,fu) 
           } else { 
      for(jk=1; jk <=nlstate ; jk++){            if (u < x) a=u; else b=u; 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            if (fu <= fw || w == x) { 
         pp[jk] += freq[jk][m][i];              v=w; 
      }              w=u; 
               fv=fw; 
     for(jk=1,pos=0; jk <=nlstate ; jk++)              fw=fu; 
       pos += pp[jk];            } else if (fu <= fv || v == x || v == w) { 
     for(jk=1; jk <=nlstate ; jk++){              v=u; 
       if(pos>=1.e-5)              fv=fu; 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            } 
       else          } 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    } 
       if( i <= (int) agemax){    nrerror("Too many iterations in brent"); 
         if(pos>=1.e-5){    *xmin=x; 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    return fx; 
           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]);*/  
         }  /****************** mnbrak ***********************/
       else  
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       }              double (*func)(double)) 
     }  { 
     for(jk=-1; jk <=nlstate+ndeath; jk++)    double ulim,u,r,q, dum;
       for(m=-1; m <=nlstate+ndeath; m++)    double fu; 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);   
     if(i <= (int) agemax)    *fa=(*func)(*ax); 
       fprintf(ficresp,"\n");    *fb=(*func)(*bx); 
     printf("\n");    if (*fb > *fa) { 
     }      SHFT(dum,*ax,*bx,dum) 
     }        SHFT(dum,*fb,*fa,dum) 
  }        } 
   dateintmean=dateintsum/k2cpt;    *cx=(*bx)+GOLD*(*bx-*ax); 
      *fc=(*func)(*cx); 
   fclose(ficresp);    while (*fb > *fc) { /* Declining fa, fb, fc */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      r=(*bx-*ax)*(*fb-*fc); 
   free_vector(pp,1,nlstate);      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   /* End of Freq */        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
 }      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
       if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
 /************ Prevalence ********************/        fu=(*func)(u); 
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)  #ifdef DEBUG
 {  /* Some frequencies */        /* f(x)=A(x-u)**2+f(u) */
          double A, fparabu; 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
   double ***freq; /* Frequencies */        fparabu= *fa - A*(*ax-u)*(*ax-u);
   double *pp;        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);
   double pos, k2;        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 
   pp=vector(1,nlstate);      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        fu=(*func)(u); 
          if (fu < *fc) { 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   j1=0;            SHFT(*fb,*fc,fu,(*func)(u)) 
              } 
   j=cptcoveff;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        u=ulim; 
          fu=(*func)(u); 
  for(k1=1; k1<=j;k1++){      } else { 
     for(i1=1; i1<=ncodemax[k1];i1++){        u=(*cx)+GOLD*(*cx-*bx); 
       j1++;        fu=(*func)(u); 
        } 
       for (i=-1; i<=nlstate+ndeath; i++)        SHFT(*ax,*bx,*cx,u) 
         for (jk=-1; jk<=nlstate+ndeath; jk++)          SHFT(*fa,*fb,*fc,fu) 
           for(m=agemin; m <= agemax+3; m++)        } 
             freq[i][jk][m]=0;  } 
        
       for (i=1; i<=imx; i++) {  /*************** linmin ************************/
         bool=1;  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
         if  (cptcovn>0) {  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
           for (z1=1; z1<=cptcoveff; z1++)  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  the value of func at the returned location p . This is actually all accomplished by calling the
               bool=0;  routines mnbrak and brent .*/
         }  int ncom; 
         if (bool==1) {  double *pcom,*xicom;
           for(m=firstpass; m<=lastpass; m++){  double (*nrfunc)(double []); 
             k2=anint[m][i]+(mint[m][i]/12.);   
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
               if(agev[m][i]==0) agev[m][i]=agemax+1;  { 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    double brent(double ax, double bx, double cx, 
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];                 double (*f)(double), double tol, double *xmin); 
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];      double f1dim(double x); 
             }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
           }                double *fc, double (*func)(double)); 
         }    int j; 
       }    double xx,xmin,bx,ax; 
          double fx,fb,fa;
         for(i=(int)agemin; i <= (int)agemax+3; i++){   
           for(jk=1; jk <=nlstate ; jk++){    ncom=n; 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    pcom=vector(1,n); 
               pp[jk] += freq[jk][m][i];    xicom=vector(1,n); 
           }    nrfunc=func; 
           for(jk=1; jk <=nlstate ; jk++){    for (j=1;j<=n;j++) { 
             for(m=-1, pos=0; m <=0 ; m++)      pcom[j]=p[j]; 
             pos += freq[jk][m][i];      xicom[j]=xi[j]; 
         }    } 
            ax=0.0; 
          for(jk=1; jk <=nlstate ; jk++){    xx=1.0; 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
              pp[jk] += freq[jk][m][i];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
          }  #ifdef DEBUG
              printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
          for(jk=1; jk <=nlstate ; jk++){              for (j=1;j<=n;j++) { 
            if( i <= (int) agemax){      xi[j] *= xmin; 
              if(pos>=1.e-5){      p[j] += xi[j]; 
                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-
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
   free_vector(pp,1,nlstate);  such that failure to decrease by more than this amount on one iteration signals doneness. On
    output, p is set to the best point found, xi is the then-current direction set, fret is the returned
 }  /* End of Freq */  function value at p , and iter is the number of iterations taken. The routine linmin is used.
    */
 /************* Waves Concatenation ***************/  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               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, 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.                double (*func)(double [])); 
      Death is a valid wave (if date is known).    int i,ibig,j; 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    double del,t,*pt,*ptt,*xit;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    double fp,fptt;
      and mw[mi+1][i]. dh depends on stepm.    double *xits;
      */    int niterf, itmp;
   
   int i, mi, m;    pt=vector(1,n); 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    ptt=vector(1,n); 
      double sum=0., jmean=0.;*/    xit=vector(1,n); 
     xits=vector(1,n); 
   int j, k=0,jk, ju, jl;    *fret=(*func)(p); 
   double sum=0.;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   jmin=1e+5;      rcurr_time = time(NULL);  
   jmax=-1;    for (*iter=1;;++(*iter)) { 
   jmean=0.;      fp=(*fret); 
   for(i=1; i<=imx; i++){      ibig=0; 
     mi=0;      del=0.0; 
     m=firstpass;      rlast_time=rcurr_time;
     while(s[m][i] <= nlstate){      /* (void) gettimeofday(&curr_time,&tzp); */
       if(s[m][i]>=1)      rcurr_time = time(NULL);  
         mw[++mi][i]=m;      curr_time = *localtime(&rcurr_time);
       if(m >=lastpass)      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
         break;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
       else  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
         m++;     for (i=1;i<=n;i++) {
     }/* end while */        printf(" %d %.12f",i, p[i]);
     if (s[m][i] > nlstate){        fprintf(ficlog," %d %.12lf",i, p[i]);
       mi++;     /* Death is another wave */        fprintf(ficrespow," %.12lf", p[i]);
       /* if(mi==0)  never been interviewed correctly before death */      }
          /* Only death is a correct wave */      printf("\n");
       mw[mi][i]=m;      fprintf(ficlog,"\n");
     }      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
     wav[i]=mi;        tml = *localtime(&rcurr_time);
     if(mi==0)        strcpy(strcurr,asctime(&tml));
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        rforecast_time=rcurr_time; 
   }        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   for(i=1; i<=imx; i++){          strcurr[itmp-1]='\0';
     for(mi=1; mi<wav[i];mi++){        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       if (stepm <=0)        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
         dh[mi][i]=1;        for(niterf=10;niterf<=30;niterf+=10){
       else{          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         if (s[mw[mi+1][i]][i] > nlstate) {          forecast_time = *localtime(&rforecast_time);
           if (agedc[i] < 2*AGESUP) {          strcpy(strfor,asctime(&forecast_time));
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          itmp = strlen(strfor);
           if(j==0) j=1;  /* Survives at least one month after exam */          if(strfor[itmp-1]=='\n')
           k=k+1;          strfor[itmp-1]='\0';
           if (j >= jmax) jmax=j;          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 <= jmin) jmin=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);
           sum=sum+j;        }
           /* if (j<10) printf("j=%d num=%d ",j,i); */      }
           }      for (i=1;i<=n;i++) { 
         }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         else{        fptt=(*fret); 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  #ifdef DEBUG
           k=k+1;            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
           if (j >= jmax) jmax=j;            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
           else if (j <= jmin)jmin=j;  #endif
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        printf("%d",i);fflush(stdout);
           sum=sum+j;        fprintf(ficlog,"%d",i);fflush(ficlog);
         }        linmin(p,xit,n,fret,func); 
         jk= j/stepm;        if (fabs(fptt-(*fret)) > del) { 
         jl= j -jk*stepm;          del=fabs(fptt-(*fret)); 
         ju= j -(jk+1)*stepm;          ibig=i; 
         if(jl <= -ju)        } 
           dh[mi][i]=jk;  #ifdef DEBUG
         else        printf("%d %.12e",i,(*fret));
           dh[mi][i]=jk+1;        fprintf(ficlog,"%d %.12e",i,(*fret));
         if(dh[mi][i]==0)        for (j=1;j<=n;j++) {
           dh[mi][i]=1; /* At least one step */          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       }          printf(" x(%d)=%.12e",j,xit[j]);
     }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   }        }
   jmean=sum/k;        for(j=1;j<=n;j++) {
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          printf(" p(%d)=%.12e",j,p[j]);
  }          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
 /*********** Tricode ****************************/        }
 void tricode(int *Tvar, int **nbcode, int imx)        printf("\n");
 {        fprintf(ficlog,"\n");
   int Ndum[20],ij=1, k, j, i;  #endif
   int cptcode=0;      } /* end i */
   cptcoveff=0;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
    #ifdef DEBUG
   for (k=0; k<19; k++) Ndum[k]=0;        int k[2],l;
   for (k=1; k<=7; k++) ncodemax[k]=0;        k[0]=1;
         k[1]=-1;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        printf("Max: %.12e",(*func)(p));
     for (i=1; i<=imx; i++) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
       ij=(int)(covar[Tvar[j]][i]);        for (j=1;j<=n;j++) {
       Ndum[ij]++;          printf(" %.12e",p[j]);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          fprintf(ficlog," %.12e",p[j]);
       if (ij > cptcode) cptcode=ij;        }
     }        printf("\n");
         fprintf(ficlog,"\n");
     for (i=0; i<=cptcode; i++) {        for(l=0;l<=1;l++) {
       if(Ndum[i]!=0) ncodemax[j]++;          for (j=1;j<=n;j++) {
     }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     ij=1;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
             fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
     for (i=1; i<=ncodemax[j]; i++) {          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       for (k=0; k<=19; k++) {          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         if (Ndum[k] != 0) {        }
           nbcode[Tvar[j]][ij]=k;  #endif
           ij++;  
         }  
         if (ij > ncodemax[j]) break;        free_vector(xit,1,n); 
       }          free_vector(xits,1,n); 
     }        free_vector(ptt,1,n); 
   }          free_vector(pt,1,n); 
         return; 
  for (k=0; k<19; k++) Ndum[k]=0;      } 
       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
  for (i=1; i<=ncovmodel-2; i++) {      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
       ij=Tvar[i];        ptt[j]=2.0*p[j]-pt[j]; 
       Ndum[ij]++;        xit[j]=p[j]-pt[j]; 
     }        pt[j]=p[j]; 
       } 
  ij=1;      fptt=(*func)(ptt); 
  for (i=1; i<=10; i++) {      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
    if((Ndum[i]!=0) && (i<=ncov)){        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
      Tvaraff[ij]=i;        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
      ij++;        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
    }        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
  }        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
          /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
     cptcoveff=ij-1;        /* Thus we compare delta(2h) with observed f1-f3 */
 }        /* or best gain on one ancient line 'del' with total  */
         /* gain f1-f2 = f1 - f2 - 'del' with del  */
 /*********** Health Expectancies ****************/        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-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)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
 {        t= t- del*SQR(fp-fptt);
   /* Health expectancies */        printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
   int i, j, nhstepm, hstepm, h;        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);
   double age, agelim,hf;  #ifdef DEBUG
   double ***p3mat;        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                 (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   fprintf(ficreseij,"# Health expectancies\n");        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   fprintf(ficreseij,"# Age");               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   for(i=1; i<=nlstate;i++)        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
     for(j=1; j<=nlstate;j++)        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);
       fprintf(ficreseij," %1d-%1d",i,j);  #endif
   fprintf(ficreseij,"\n");        if (t < 0.0) { /* Then we use it for last direction */
           linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
   hstepm=1*YEARM; /*  Every j years of age (in month) */          for (j=1;j<=n;j++) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
             xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
   agelim=AGESUP;          }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
     /* nhstepm age range expressed in number of stepm */          fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years = 20*12/6=40 stepm */  #ifdef DEBUG
     if (stepm >= YEARM) hstepm=1;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(j=1;j<=n;j++){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            printf(" %.12e",xit[j]);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            fprintf(ficlog," %.12e",xit[j]);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            }
           printf("\n");
           fprintf(ficlog,"\n");
     for(i=1; i<=nlstate;i++)  #endif
       for(j=1; j<=nlstate;j++)        } /* end of t negative */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){      } /* end if (fptt < fp)  */
           eij[i][j][(int)age] +=p3mat[i][j][h];    } 
         }  } 
      
     hf=1;  /**** Prevalence limit (stable or period prevalence)  ****************/
     if (stepm >= YEARM) hf=stepm/YEARM;  
     fprintf(ficreseij,"%.0f",age );  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     for(i=1; i<=nlstate;i++)  {
       for(j=1; j<=nlstate;j++){    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);       matrix by transitions matrix until convergence is reached */
       }    
     fprintf(ficreseij,"\n");    int i, ii,j,k;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double min, max, maxmin, maxmax,sumnew=0.;
   }    /* double **matprod2(); */ /* test */
 }    double **out, cov[NCOVMAX+1], **pmij();
     double **newm;
 /************ Variance ******************/    double agefin, delaymax=50 ; /* Max number of years to converge */
 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)    
 {    for (ii=1;ii<=nlstate+ndeath;ii++)
   /* Variance of health expectancies */      for (j=1;j<=nlstate+ndeath;j++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **newm;      }
   double **dnewm,**doldm;    
   int i, j, nhstepm, hstepm, h;    cov[1]=1.;
   int k, cptcode;    
   double *xp;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   double **gp, **gm;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   double ***gradg, ***trgradg;      newm=savm;
   double ***p3mat;      /* Covariates have to be included here again */
   double age,agelim;      cov[2]=agefin;
   int theta;      
       for (k=1; k<=cptcovn;k++) {
    fprintf(ficresvij,"# Covariances of life expectancies\n");        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   fprintf(ficresvij,"# Age");        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
   for(i=1; i<=nlstate;i++)      }
     for(j=1; j<=nlstate;j++)      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
   fprintf(ficresvij,"\n");      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
       
   xp=vector(1,npar);      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   dnewm=matrix(1,nlstate,1,npar);      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   doldm=matrix(1,nlstate,1,nlstate);      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
        /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   hstepm=1*YEARM; /* Every year of age */      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
   agelim = AGESUP;      
   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;      maxmax=0.;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for(j=1;j<=nlstate;j++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        min=1.;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        max=0.;
     gp=matrix(0,nhstepm,1,nlstate);        for(i=1; i<=nlstate; i++) {
     gm=matrix(0,nhstepm,1,nlstate);          sumnew=0;
           for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     for(theta=1; theta <=npar; theta++){          prlim[i][j]= newm[i][j]/(1-sumnew);
       for(i=1; i<=npar; i++){ /* Computes gradient */          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          max=FMAX(max,prlim[i][j]);
       }          min=FMIN(min,prlim[i][j]);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
       if (popbased==1) {      } /* j loop */
         for(i=1; i<=nlstate;i++)      if(maxmax < ftolpl){
           prlim[i][i]=probs[(int)age][i][ij];        return prlim;
       }      }
          } /* age loop */
       for(j=1; j<= nlstate; j++){    return prlim; /* should not reach here */
         for(h=0; h<=nhstepm; h++){  }
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  /*************** transition probabilities ***************/ 
         }  
       }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
      {
       for(i=1; i<=npar; i++) /* Computes gradient */    /* According to parameters values stored in x and the covariate's values stored in cov,
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       computes the probability to be observed in state j being in state i by appying the
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);         model to the ncovmodel covariates (including constant and age).
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       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
       if (popbased==1) {       ncth covariate in the global vector x is given by the formula:
         for(i=1; i<=nlstate;i++)       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
           prlim[i][i]=probs[(int)age][i][ij];       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
       }       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
        sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
       for(j=1; j<= nlstate; j++){       Outputs ps[i][j] the probability to be observed in j being in j according to
         for(h=0; h<=nhstepm; h++){       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    double s1, lnpijopii;
         }    /*double t34;*/
       }    int i,j, nc, ii, jj;
   
       for(j=1; j<= nlstate; j++)      for(i=1; i<= nlstate; i++){
         for(h=0; h<=nhstepm; h++){        for(j=1; j<i;j++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         }            /*lnpijopii += param[i][j][nc]*cov[nc];*/
     } /* End theta */            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
   /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     for(h=0; h<=nhstepm; h++)  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       for(j=1; j<=nlstate;j++)        }
         for(theta=1; theta <=npar; theta++)        for(j=i+1; j<=nlstate+ndeath;j++){
           trgradg[h][j][theta]=gradg[h][theta][j];          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
             /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     for(i=1;i<=nlstate;i++)            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
       for(j=1;j<=nlstate;j++)  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
         vareij[i][j][(int)age] =0.;          }
     for(h=0;h<=nhstepm;h++){          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       for(k=0;k<=nhstepm;k++){        }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      }
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      
         for(i=1;i<=nlstate;i++)      for(i=1; i<= nlstate; i++){
           for(j=1;j<=nlstate;j++)        s1=0;
             vareij[i][j][(int)age] += doldm[i][j];        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); */
     h=1;        }
     if (stepm >= YEARM) h=stepm/YEARM;        for(j=i+1; j<=nlstate+ndeath; j++){
     fprintf(ficresvij,"%.0f ",age );          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++){        }
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       }        ps[i][i]=1./(s1+1.);
     fprintf(ficresvij,"\n");        /* Computing other pijs */
     free_matrix(gp,0,nhstepm,1,nlstate);        for(j=1; j<i; j++)
     free_matrix(gm,0,nhstepm,1,nlstate);          ps[i][j]= exp(ps[i][j])*ps[i][i];
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        for(j=i+1; j<=nlstate+ndeath; j++)
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          ps[i][j]= exp(ps[i][j])*ps[i][i];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   } /* End age */      } /* end i */
        
   free_vector(xp,1,npar);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   free_matrix(doldm,1,nlstate,1,npar);        for(jj=1; jj<= nlstate+ndeath; jj++){
   free_matrix(dnewm,1,nlstate,1,nlstate);          ps[ii][jj]=0;
           ps[ii][ii]=1;
 }        }
       }
 /************ Variance of prevlim ******************/      
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)      
 {      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
   /* Variance of prevalence limit */      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
   double **newm;      /*   } */
   double **dnewm,**doldm;      /*   printf("\n "); */
   int i, j, nhstepm, hstepm;      /* } */
   int k, cptcode;      /* printf("\n ");printf("%lf ",cov[2]);*/
   double *xp;      /*
   double *gp, *gm;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   double **gradg, **trgradg;        goto end;*/
   double age,agelim;      return ps;
   int theta;  }
      
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  /**************** Product of 2 matrices ******************/
   fprintf(ficresvpl,"# Age");  
   for(i=1; i<=nlstate;i++)  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
       fprintf(ficresvpl," %1d-%1d",i,i);  {
   fprintf(ficresvpl,"\n");    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
        b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   xp=vector(1,npar);    /* in, b, out are matrice of pointers which should have been initialized 
   dnewm=matrix(1,nlstate,1,npar);       before: only the contents of out is modified. The function returns
   doldm=matrix(1,nlstate,1,nlstate);       a pointer to pointers identical to out */
      int i, j, k;
   hstepm=1*YEARM; /* Every year of age */    for(i=nrl; i<= nrh; i++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for(k=ncolol; k<=ncoloh; k++){
   agelim = AGESUP;        out[i][k]=0.;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        for(j=ncl; j<=nch; j++)
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          out[i][k] +=in[i][j]*b[j][k];
     if (stepm >= YEARM) hstepm=1;      }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    return out;
     gradg=matrix(1,npar,1,nlstate);  }
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);  
   /************* Higher Matrix Product ***************/
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  {
       }    /* Computes the transition matrix starting at age 'age' over 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       'nhstepm*hstepm*stepm' months (i.e. until
       for(i=1;i<=nlstate;i++)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         gp[i] = prlim[i][i];       nhstepm*hstepm matrices. 
           Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       for(i=1; i<=npar; i++) /* Computes gradient */       (typically every 2 years instead of every month which is too big 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       for the memory).
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       Model is determined by parameters x and covariates have to be 
       for(i=1;i<=nlstate;i++)       included manually here. 
         gm[i] = prlim[i][i];  
        */
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    int i, j, d, h, k;
     } /* End theta */    double **out, cov[NCOVMAX+1];
     double **newm;
     trgradg =matrix(1,nlstate,1,npar);  
     /* Hstepm could be zero and should return the unit matrix */
     for(j=1; j<=nlstate;j++)    for (i=1;i<=nlstate+ndeath;i++)
       for(theta=1; theta <=npar; theta++)      for (j=1;j<=nlstate+ndeath;j++){
         trgradg[j][theta]=gradg[theta][j];        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
     for(i=1;i<=nlstate;i++)      }
       varpl[i][(int)age] =0.;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    for(h=1; h <=nhstepm; h++){
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      for(d=1; d <=hstepm; d++){
     for(i=1;i<=nlstate;i++)        newm=savm;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        /* Covariates have to be included here again */
         cov[1]=1.;
     fprintf(ficresvpl,"%.0f ",age );        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     for(i=1; i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     fprintf(ficresvpl,"\n");        for (k=1; k<=cptcovage;k++)
     free_vector(gp,1,nlstate);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     free_vector(gm,1,nlstate);        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
     free_matrix(gradg,1,npar,1,nlstate);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   free_vector(xp,1,npar);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   free_matrix(doldm,1,nlstate,1,npar);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   free_matrix(dnewm,1,nlstate,1,nlstate);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
 }        oldm=newm;
       }
 /************ Variance of one-step probabilities  ******************/      for(i=1; i<=nlstate+ndeath; i++)
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        for(j=1;j<=nlstate+ndeath;j++) {
 {          po[i][j][h]=newm[i][j];
   int i, j;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   int k=0, cptcode;        }
   double **dnewm,**doldm;      /*printf("h=%d ",h);*/
   double *xp;    } /* end h */
   double *gp, *gm;  /*     printf("\n H=%d \n",h); */
   double **gradg, **trgradg;    return po;
   double age,agelim, cov[NCOVMAX];  }
   int theta;  
   char fileresprob[FILENAMELENGTH];  #ifdef NLOPT
     double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
   strcpy(fileresprob,"prob");    double fret;
   strcat(fileresprob,fileres);    double *xt;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    int j;
     printf("Problem with resultfile: %s\n", fileresprob);    myfunc_data *d2 = (myfunc_data *) pd;
   }  /* xt = (p1-1); */
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    xt=vector(1,n); 
      for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
   
   xp=vector(1,npar);    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    printf("Function = %.12lf ",fret);
      for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
   cov[1]=1;    printf("\n");
   for (age=bage; age<=fage; age ++){   free_vector(xt,1,n);
     cov[2]=age;    return fret;
     gradg=matrix(1,npar,1,9);  }
     trgradg=matrix(1,9,1,npar);  #endif
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  /*************** log-likelihood *************/
      double func( double *x)
     for(theta=1; theta <=npar; theta++){  {
       for(i=1; i<=npar; i++)    int i, ii, j, k, mi, d, kk;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
          double **out;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    double sw; /* Sum of weights */
        double lli; /* Individual log likelihood */
       k=0;    int s1, s2;
       for(i=1; i<= (nlstate+ndeath); i++){    double bbh, survp;
         for(j=1; j<=(nlstate+ndeath);j++){    long ipmx;
            k=k+1;    /*extern weight */
           gp[k]=pmmij[i][j];    /* We are differentiating ll according to initial status */
         }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       }    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
       for(i=1; i<=npar; i++)    */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
        ++countcallfunc;
   
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    cov[1]=1.;
       k=0;  
       for(i=1; i<=(nlstate+ndeath); i++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
         for(j=1; j<=(nlstate+ndeath);j++){  
           k=k+1;    if(mle==1){
           gm[k]=pmmij[i][j];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        /* Computes the values of the ncovmodel covariates of the model
       }           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
                 Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)           to be observed in j being in i according to the model.
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];           */
     }        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
           cov[2+k]=covar[Tvar[k]][i];
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        }
       for(theta=1; theta <=npar; theta++)        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
       trgradg[j][theta]=gradg[theta][j];           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
             has been calculated etc */
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        for(mi=1; mi<= wav[i]-1; mi++){
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
      pmij(pmmij,cov,ncovmodel,x,nlstate);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
      k=0;            }
      for(i=1; i<=(nlstate+ndeath); i++){          for(d=0; d<dh[mi][i]; d++){
        for(j=1; j<=(nlstate+ndeath);j++){            newm=savm;
          k=k+1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
          gm[k]=pmmij[i][j];            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 */
      }            }
                  out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      /*printf("\n%d ",(int)age);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            savm=oldm;
                    oldm=newm;
           } /* end mult */
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        
      }*/          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
   fprintf(ficresprob,"\n%d ",(int)age);           * 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 (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){           * the nearest (and in case of equal distance, to the lowest) interval but now
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);           * (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
            * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));           * -stepm/2 to stepm/2 .
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));           * For stepm=1 the results are the same as for previous versions of Imach.
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);           * For stepm > 1 the results are less biased than in previous versions. 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);           */
 }          s1=s[mw[mi][i]][i];
  free_vector(xp,1,npar);          s2=s[mw[mi+1][i]][i];
 fclose(ficresprob);          bbh=(double)bh[mi][i]/(double)stepm; 
  exit(0);          /* bias bh is positive if real duration
 }           * is higher than the multiple of stepm and negative otherwise.
            */
 /***********************************************/          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 /**************** Main Program *****************/          if( s2 > nlstate){ 
 /***********************************************/            /* i.e. if s2 is a death state and if the date of death is known 
                then the contribution to the likelihood is the probability to 
 int main(int argc, char *argv[])               die between last step unit time and current  step unit time, 
 {               which is also equal to probability to die before dh 
                minus probability to die before dh-stepm . 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;               In version up to 0.92 likelihood was computed
   double agedeb, agefin,hf;          as if date of death was unknown. Death was treated as any other
   double agemin=1.e20, agemax=-1.e20;          health state: the date of the interview describes the actual state
           and not the date of a change in health state. The former idea was
   double fret;          to consider that at each interview the state was recorded
   double **xi,tmp,delta;          (healthy, disable or death) and IMaCh was corrected; but when we
           introduced the exact date of death then we should have modified
   double dum; /* Dummy variable */          the contribution of an exact death to the likelihood. This new
   double ***p3mat;          contribution is smaller and very dependent of the step unit
   int *indx;          stepm. It is no more the probability to die between last interview
   char line[MAXLINE], linepar[MAXLINE];          and month of death but the probability to survive from last
   char title[MAXLINE];          interview up to one month before death multiplied by the
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];          probability to die within a month. Thanks to Chris
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          Jackson for correcting this bug.  Former versions increased
            mortality artificially. The bad side is that we add another loop
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];;          which slows down the processing. The difference can be up to 10%
           lower mortality.
   char filerest[FILENAMELENGTH];            */
   char fileregp[FILENAMELENGTH];            lli=log(out[s1][s2] - savm[s1][s2]);
   char popfile[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  
   int firstobs=1, lastobs=10;          } else if  (s2==-2) {
   int sdeb, sfin; /* Status at beginning and end */            for (j=1,survp=0. ; j<=nlstate; j++) 
   int c,  h , cpt,l;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   int ju,jl, mi;            /*survp += out[s1][j]; */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            lli= log(survp);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          }
   int mobilav=0,popforecast=0;          
   int hstepm, nhstepm;          else if  (s2==-4) { 
   int *popage;/*boolprev=0 if date and zero if wave*/            for (j=3,survp=0. ; j<=nlstate; j++)  
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
   double bage, fage, age, agelim, agebase;          } 
   double ftolpl=FTOL;  
   double **prlim;          else if  (s2==-5) { 
   double *severity;            for (j=1,survp=0. ; j<=2; j++)  
   double ***param; /* Matrix of parameters */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double  *p;            lli= log(survp); 
   double **matcov; /* Matrix of covariance */          } 
   double ***delti3; /* Scale */          
   double *delti; /* Scale */          else{
   double ***eij, ***vareij;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double **varpl; /* Variances of prevalence limits by age */            /*  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 */
   double *epj, vepp;          } 
   double kk1, kk2;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double *popeffectif,*popcount;          /*if(lli ==000.0)*/
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;          /*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); */
   double yp,yp1,yp2;          ipmx +=1;
           sw += weight[i];
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char *alph[]={"a","a","b","c","d","e"}, str[4];        } /* end of wave */
       } /* end of individual */
     }  else if(mle==2){
   char z[1]="c", occ;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 #include <sys/time.h>        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 #include <time.h>        for(mi=1; mi<= wav[i]-1; mi++){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   /* long total_usecs;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   struct timeval start_time, end_time;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   printf("\n%s",version);            for (kk=1; kk<=cptcovage;kk++) {
   if(argc <=1){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     printf("\nEnter the parameter file name: ");            }
     scanf("%s",pathtot);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   else{            savm=oldm;
     strcpy(pathtot,argv[1]);            oldm=newm;
   }          } /* end mult */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        
   /*cygwin_split_path(pathtot,path,optionfile);          s1=s[mw[mi][i]][i];
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          s2=s[mw[mi+1][i]][i];
   /* cutv(path,optionfile,pathtot,'\\');*/          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);          ipmx +=1;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          sw += weight[i];
   chdir(path);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   replace(pathc,path);        } /* end of wave */
       } /* end of individual */
 /*-------- arguments in the command line --------*/    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcpy(fileres,"r");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   strcat(fileres, optionfilefiname);        for(mi=1; mi<= wav[i]-1; mi++){
   strcat(fileres,".txt");    /* Other files have txt extension */          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   /*---------arguments file --------*/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {            }
     printf("Problem with optionfile %s\n",optionfile);          for(d=0; d<dh[mi][i]; d++){
     goto end;            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   strcpy(filereso,"o");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   strcat(filereso,fileres);            }
   if((ficparo=fopen(filereso,"w"))==NULL) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     printf("Problem with Output resultfile: %s\n", filereso);goto end;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
             oldm=newm;
   /* Reads comments: lines beginning with '#' */          } /* end mult */
   while((c=getc(ficpar))=='#' && c!= EOF){        
     ungetc(c,ficpar);          s1=s[mw[mi][i]][i];
     fgets(line, MAXLINE, ficpar);          s2=s[mw[mi+1][i]][i];
     puts(line);          bbh=(double)bh[mi][i]/(double)stepm; 
     fputs(line,ficparo);          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   }          ipmx +=1;
   ungetc(c,ficpar);          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        } /* end of wave */
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);      } /* end of individual */
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
 while((c=getc(ficpar))=='#' && c!= EOF){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     ungetc(c,ficpar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fgets(line, MAXLINE, ficpar);        for(mi=1; mi<= wav[i]-1; mi++){
     puts(line);          for (ii=1;ii<=nlstate+ndeath;ii++)
     fputs(line,ficparo);            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   ungetc(c,ficpar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
              for(d=0; d<dh[mi][i]; d++){
   covar=matrix(0,NCOVMAX,1,n);            newm=savm;
   cptcovn=0;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   ncovmodel=2+cptcovn;            }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* Read guess parameters */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* Reads comments: lines beginning with '#' */            savm=oldm;
   while((c=getc(ficpar))=='#' && c!= EOF){            oldm=newm;
     ungetc(c,ficpar);          } /* end mult */
     fgets(line, MAXLINE, ficpar);        
     puts(line);          s1=s[mw[mi][i]][i];
     fputs(line,ficparo);          s2=s[mw[mi+1][i]][i];
   }          if( s2 > nlstate){ 
   ungetc(c,ficpar);            lli=log(out[s1][s2] - savm[s1][s2]);
            }else{
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for(i=1; i <=nlstate; i++)          }
     for(j=1; j <=nlstate+ndeath-1; j++){          ipmx +=1;
       fscanf(ficpar,"%1d%1d",&i1,&j1);          sw += weight[i];
       fprintf(ficparo,"%1d%1d",i1,j1);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       printf("%1d%1d",i,j);  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       for(k=1; k<=ncovmodel;k++){        } /* end of wave */
         fscanf(ficpar," %lf",&param[i][j][k]);      } /* end of individual */
         printf(" %lf",param[i][j][k]);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         fprintf(ficparo," %lf",param[i][j][k]);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       fscanf(ficpar,"\n");        for(mi=1; mi<= wav[i]-1; mi++){
       printf("\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
       fprintf(ficparo,"\n");            for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            }
           for(d=0; d<dh[mi][i]; d++){
   p=param[1][1];            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* Reads comments: lines beginning with '#' */            for (kk=1; kk<=cptcovage;kk++) {
   while((c=getc(ficpar))=='#' && c!= EOF){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);          
     puts(line);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     fputs(line,ficparo);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
   ungetc(c,ficpar);            oldm=newm;
           } /* end mult */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          s1=s[mw[mi][i]][i];
   for(i=1; i <=nlstate; i++){          s2=s[mw[mi+1][i]][i];
     for(j=1; j <=nlstate+ndeath-1; j++){          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       fscanf(ficpar,"%1d%1d",&i1,&j1);          ipmx +=1;
       printf("%1d%1d",i,j);          sw += weight[i];
       fprintf(ficparo,"%1d%1d",i1,j1);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(k=1; k<=ncovmodel;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]);*/
         fscanf(ficpar,"%le",&delti3[i][j][k]);        } /* end of wave */
         printf(" %le",delti3[i][j][k]);      } /* end of individual */
         fprintf(ficparo," %le",delti3[i][j][k]);    } /* End of if */
       }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       fscanf(ficpar,"\n");    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       printf("\n");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       fprintf(ficparo,"\n");    return -l;
     }  }
   }  
   delti=delti3[1][1];  /*************** log-likelihood *************/
    double funcone( double *x)
   /* Reads comments: lines beginning with '#' */  {
   while((c=getc(ficpar))=='#' && c!= EOF){    /* Same as likeli but slower because of a lot of printf and if */
     ungetc(c,ficpar);    int i, ii, j, k, mi, d, kk;
     fgets(line, MAXLINE, ficpar);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     puts(line);    double **out;
     fputs(line,ficparo);    double lli; /* Individual log likelihood */
   }    double llt;
   ungetc(c,ficpar);    int s1, s2;
      double bbh, survp;
   matcov=matrix(1,npar,1,npar);    /*extern weight */
   for(i=1; i <=npar; i++){    /* We are differentiating ll according to initial status */
     fscanf(ficpar,"%s",&str);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     printf("%s",str);    /*for(i=1;i<imx;i++) 
     fprintf(ficparo,"%s",str);      printf(" %d\n",s[4][i]);
     for(j=1; j <=i; j++){    */
       fscanf(ficpar," %le",&matcov[i][j]);    cov[1]=1.;
       printf(" %.5le",matcov[i][j]);  
       fprintf(ficparo," %.5le",matcov[i][j]);    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
     fscanf(ficpar,"\n");    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     printf("\n");      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fprintf(ficparo,"\n");      for(mi=1; mi<= wav[i]-1; mi++){
   }        for (ii=1;ii<=nlstate+ndeath;ii++)
   for(i=1; i <=npar; i++)          for (j=1;j<=nlstate+ndeath;j++){
     for(j=i+1;j<=npar;j++)            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       matcov[i][j]=matcov[j][i];            savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   printf("\n");        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     /*-------- data file ----------*/          for (kk=1; kk<=cptcovage;kk++) {
     if((ficres =fopen(fileres,"w"))==NULL) {            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       printf("Problem with resultfile: %s\n", fileres);goto end;          }
     }          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     fprintf(ficres,"#%s\n",version);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     if((fic=fopen(datafile,"r"))==NULL)    {          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
       printf("Problem with datafile: %s\n", datafile);goto end;          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
     }          savm=oldm;
           oldm=newm;
     n= lastobs;        } /* end mult */
     severity = vector(1,maxwav);        
     outcome=imatrix(1,maxwav+1,1,n);        s1=s[mw[mi][i]][i];
     num=ivector(1,n);        s2=s[mw[mi+1][i]][i];
     moisnais=vector(1,n);        bbh=(double)bh[mi][i]/(double)stepm; 
     annais=vector(1,n);        /* bias is positive if real duration
     moisdc=vector(1,n);         * is higher than the multiple of stepm and negative otherwise.
     andc=vector(1,n);         */
     agedc=vector(1,n);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     cod=ivector(1,n);          lli=log(out[s1][s2] - savm[s1][s2]);
     weight=vector(1,n);        } else if  (s2==-2) {
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          for (j=1,survp=0. ; j<=nlstate; j++) 
     mint=matrix(1,maxwav,1,n);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     anint=matrix(1,maxwav,1,n);          lli= log(survp);
     s=imatrix(1,maxwav+1,1,n);        }else if (mle==1){
     adl=imatrix(1,maxwav+1,1,n);              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     tab=ivector(1,NCOVMAX);        } else if(mle==2){
     ncodemax=ivector(1,8);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         } else if(mle==3){  /* exponential inter-extrapolation */
     i=1;          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     while (fgets(line, MAXLINE, fic) != NULL)    {        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       if ((i >= firstobs) && (i <=lastobs)) {          lli=log(out[s1][s2]); /* Original formula */
                } else{  /* mle=0 back to 1 */
         for (j=maxwav;j>=1;j--){          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          /*lli=log(out[s1][s2]); */ /* Original formula */
           strcpy(line,stra);        } /* End of if */
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        ipmx +=1;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        sw += weight[i];
         }        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        if(globpr){
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
    %11.6f %11.6f %11.6f ", \
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);            llt +=ll[k]*gipmx/gsw;
         for (j=ncov;j>=1;j--){            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          }
         }          fprintf(ficresilk," %10.6f\n", -llt);
         num[i]=atol(stra);        }
              } /* end of wave */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    } /* end of individual */
           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;}*/    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         i=i+1;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       }    if(globpr==0){ /* First time we count the contributions and weights */
     }      gipmx=ipmx;
     /* printf("ii=%d", ij);      gsw=sw;
        scanf("%d",i);*/    }
   imx=i-1; /* Number of individuals */    return -l;
   }
   /* for (i=1; i<=imx; i++){  
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;  
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;  /*************** function likelione ***********/
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     }  {
     /* This routine should help understanding what is done with 
     for (i=1; i<=imx; i++)       the selection of individuals/waves and
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/       to check the exact contribution to the likelihood.
        Plotting could be done.
   /* Calculation of the number of parameter from char model*/     */
   Tvar=ivector(1,15);    int k;
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);    if(*globpri !=0){ /* Just counts and sums, no printings */
   Tvard=imatrix(1,15,1,2);      strcpy(fileresilk,"ilk"); 
   Tage=ivector(1,15);            strcat(fileresilk,fileres);
          if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   if (strlen(model) >1){        printf("Problem with resultfile: %s\n", fileresilk);
     j=0, j1=0, k1=1, k2=1;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     j=nbocc(model,'+');      }
     j1=nbocc(model,'*');      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");
     cptcovn=j+1;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     cptcovprod=j1;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
          for(k=1; k<=nlstate; k++) 
            fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     strcpy(modelsav,model);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    }
       printf("Error. Non available option model=%s ",model);  
       goto end;    *fretone=(*funcone)(p);
     }    if(*globpri !=0){
          fclose(ficresilk);
     for(i=(j+1); i>=1;i--){      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       cutv(stra,strb,modelsav,'+');      fflush(fichtm); 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    } 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    return;
       /*scanf("%d",i);*/  }
       if (strchr(strb,'*')) {  
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {  /*********** Maximum Likelihood Estimation ***************/
           cptcovprod--;  
           cutv(strb,stre,strd,'V');  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
           Tvar[i]=atoi(stre);  {
           cptcovage++;    int i,j, iter=0;
             Tage[cptcovage]=i;    double **xi;
             /*printf("stre=%s ", stre);*/    double fret;
         }    double fretone; /* Only one call to likelihood */
         else if (strcmp(strd,"age")==0) {    /*  char filerespow[FILENAMELENGTH];*/
           cptcovprod--;  
           cutv(strb,stre,strc,'V');  #ifdef NLOPT
           Tvar[i]=atoi(stre);    int creturn;
           cptcovage++;    nlopt_opt opt;
           Tage[cptcovage]=i;    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
         }    double *lb;
         else {    double minf; /* the minimum objective value, upon return */
           cutv(strb,stre,strc,'V');    double * p1; /* Shifted parameters from 0 instead of 1 */
           Tvar[i]=ncov+k1;    myfunc_data dinst, *d = &dinst;
           cutv(strb,strc,strd,'V');  #endif
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);  
           Tvard[k1][2]=atoi(stre);    xi=matrix(1,npar,1,npar);
           Tvar[cptcovn+k2]=Tvard[k1][1];    for (i=1;i<=npar;i++)
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      for (j=1;j<=npar;j++)
           for (k=1; k<=lastobs;k++)        xi[i][j]=(i==j ? 1.0 : 0.0);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    printf("Powell\n");  fprintf(ficlog,"Powell\n");
           k1++;    strcpy(filerespow,"pow"); 
           k2=k2+2;    strcat(filerespow,fileres);
         }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       }      printf("Problem with resultfile: %s\n", filerespow);
       else {      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    }
        /*  scanf("%d",i);*/    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       cutv(strd,strc,strb,'V');    for (i=1;i<=nlstate;i++)
       Tvar[i]=atoi(strc);      for(j=1;j<=nlstate+ndeath;j++)
       }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       strcpy(modelsav,stra);      fprintf(ficrespow,"\n");
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  #ifdef POWELL
         scanf("%d",i);*/    powell(p,xi,npar,ftol,&iter,&fret,func);
     }  #endif
 }  
    #ifdef NLOPT
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  #ifdef NEWUOA
   printf("cptcovprod=%d ", cptcovprod);    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   scanf("%d ",i);*/  #else
     fclose(fic);    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   #endif
     /*  if(mle==1){*/    lb=vector(0,npar-1);
     if (weightopt != 1) { /* Maximisation without weights*/    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
       for(i=1;i<=n;i++) weight[i]=1.0;    nlopt_set_lower_bounds(opt, lb);
     }    nlopt_set_initial_step1(opt, 0.1);
     /*-calculation of age at interview from date of interview and age at death -*/    
     agev=matrix(1,maxwav,1,imx);    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     d->function = func;
    for (i=1; i<=imx; i++)    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
      for(m=2; (m<= maxwav); m++)    nlopt_set_min_objective(opt, myfunc, d);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    nlopt_set_xtol_rel(opt, ftol);
          anint[m][i]=9999;    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
          s[m][i]=-1;      printf("nlopt failed! %d\n",creturn); 
        }    }
        else {
     for (i=1; i<=imx; i++)  {      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       for(m=1; (m<= maxwav); m++){      iter=1; /* not equal */
         if(s[m][i] >0){    }
           if (s[m][i] == nlstate+1) {    nlopt_destroy(opt);
             if(agedc[i]>0)  #endif
               if(moisdc[i]!=99 && andc[i]!=9999)    free_matrix(xi,1,npar,1,npar);
               agev[m][i]=agedc[i];    fclose(ficrespow);
             else {    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
               if (andc[i]!=9999){    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
               agev[m][i]=-1;  
               }  }
             }  
           }  /**** Computes Hessian and covariance matrix ***/
           else if(s[m][i] !=9){ /* Should no more exist */  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  {
             if(mint[m][i]==99 || anint[m][i]==9999)    double  **a,**y,*x,pd;
               agev[m][i]=1;    double **hess;
             else if(agev[m][i] <agemin){    int i, j;
               agemin=agev[m][i];    int *indx;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  
             }    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
             else if(agev[m][i] >agemax){    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
               agemax=agev[m][i];    void lubksb(double **a, int npar, int *indx, double b[]) ;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    void ludcmp(double **a, int npar, int *indx, double *d) ;
             }    double gompertz(double p[]);
             /*agev[m][i]=anint[m][i]-annais[i];*/    hess=matrix(1,npar,1,npar);
             /*   agev[m][i] = age[i]+2*m;*/  
           }    printf("\nCalculation of the hessian matrix. Wait...\n");
           else { /* =9 */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
             agev[m][i]=1;    for (i=1;i<=npar;i++){
             s[m][i]=-1;      printf("%d",i);fflush(stdout);
           }      fprintf(ficlog,"%d",i);fflush(ficlog);
         }     
         else /*= 0 Unknown */       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
           agev[m][i]=1;      
       }      /*  printf(" %f ",p[i]);
              printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }    }
     for (i=1; i<=imx; i++)  {    
       for(m=1; (m<= maxwav); m++){    for (i=1;i<=npar;i++) {
         if (s[m][i] > (nlstate+ndeath)) {      for (j=1;j<=npar;j++)  {
           printf("Error: Wrong value in nlstate or ndeath\n");          if (j>i) { 
           goto end;          printf(".%d%d",i,j);fflush(stdout);
         }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       }          hess[i][j]=hessij(p,delti,i,j,func,npar);
     }          
           hess[j][i]=hess[i][j];    
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          /*printf(" %lf ",hess[i][j]);*/
         }
     free_vector(severity,1,maxwav);      }
     free_imatrix(outcome,1,maxwav+1,1,n);    }
     free_vector(moisnais,1,n);    printf("\n");
     free_vector(annais,1,n);    fprintf(ficlog,"\n");
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     free_vector(moisdc,1,n);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     free_vector(andc,1,n);    
     a=matrix(1,npar,1,npar);
        y=matrix(1,npar,1,npar);
     wav=ivector(1,imx);    x=vector(1,npar);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    indx=ivector(1,npar);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    for (i=1;i<=npar;i++)
          for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     /* Concatenates waves */    ludcmp(a,npar,indx,&pd);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
     for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
       Tcode=ivector(1,100);      x[j]=1;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      lubksb(a,npar,indx,x);
       ncodemax[1]=1;      for (i=1;i<=npar;i++){ 
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        matcov[i][j]=x[i];
            }
    codtab=imatrix(1,100,1,10);    }
    h=0;  
    m=pow(2,cptcoveff);    printf("\n#Hessian matrix#\n");
      fprintf(ficlog,"\n#Hessian matrix#\n");
    for(k=1;k<=cptcoveff; k++){    for (i=1;i<=npar;i++) { 
      for(i=1; i <=(m/pow(2,k));i++){      for (j=1;j<=npar;j++) { 
        for(j=1; j <= ncodemax[k]; j++){        printf("%.3e ",hess[i][j]);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        fprintf(ficlog,"%.3e ",hess[i][j]);
            h++;      }
            if (h>m) h=1;codtab[h][k]=j;      printf("\n");
          }      fprintf(ficlog,"\n");
        }    }
      }  
    }    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
    /*for(i=1; i <=m ;i++){    ludcmp(a,npar,indx,&pd);
      for(k=1; k <=cptcovn; k++){  
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    /*  printf("\n#Hessian matrix recomputed#\n");
      }  
      printf("\n");    for (j=1;j<=npar;j++) {
    }      for (i=1;i<=npar;i++) x[i]=0;
    scanf("%d",i);*/      x[j]=1;
          lubksb(a,npar,indx,x);
    /* Calculates basic frequencies. Computes observed prevalence at single age      for (i=1;i<=npar;i++){ 
        and prints on file fileres'p'. */        y[i][j]=x[i];
         printf("%.3e ",y[i][j]);
            fprintf(ficlog,"%.3e ",y[i][j]);
          }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      printf("\n");
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficlog,"\n");
     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 */  
          free_matrix(a,1,npar,1,npar);
     /* For Powell, parameters are in a vector p[] starting at p[1]    free_matrix(y,1,npar,1,npar);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    free_vector(x,1,npar);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }  }
      
     /*--------- results files --------------*/  /*************** hessian matrix ****************/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
    {
     int i;
    jk=1;    int l=1, lmax=20;
    fprintf(ficres,"# Parameters\n");    double k1,k2;
    printf("# Parameters\n");    double p2[MAXPARM+1]; /* identical to x */
    for(i=1,jk=1; i <=nlstate; i++){    double res;
      for(k=1; k <=(nlstate+ndeath); k++){    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
        if (k != i)    double fx;
          {    int k=0,kmax=10;
            printf("%d%d ",i,k);    double l1;
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){    fx=func(x);
              printf("%f ",p[jk]);    for (i=1;i<=npar;i++) p2[i]=x[i];
              fprintf(ficres,"%f ",p[jk]);    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
              jk++;      l1=pow(10,l);
            }      delts=delt;
            printf("\n");      for(k=1 ; k <kmax; k=k+1){
            fprintf(ficres,"\n");        delt = delta*(l1*k);
          }        p2[theta]=x[theta] +delt;
      }        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
    }        p2[theta]=x[theta]-delt;
  if(mle==1){        k2=func(p2)-fx;
     /* Computing hessian and covariance matrix */        /*res= (k1-2.0*fx+k2)/delt/delt; */
     ftolhess=ftol; /* Usually correct */        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     hesscov(matcov, p, npar, delti, ftolhess, func);        
  }  #ifdef DEBUGHESS
     fprintf(ficres,"# Scales\n");        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);
     printf("# Scales\n");        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);
      for(i=1,jk=1; i <=nlstate; i++){  #endif
       for(j=1; j <=nlstate+ndeath; j++){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if (j!=i) {        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           fprintf(ficres,"%1d%1d",i,j);          k=kmax;
           printf("%1d%1d",i,j);        }
           for(k=1; k<=ncovmodel;k++){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
             printf(" %.5e",delti[jk]);          k=kmax; l=lmax*10;
             fprintf(ficres," %.5e",delti[jk]);        }
             jk++;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           }          delts=delt;
           printf("\n");        }
           fprintf(ficres,"\n");      }
         }    }
       }    delti[theta]=delts;
      }    return res; 
        
     k=1;  }
     fprintf(ficres,"# Covariance\n");  
     printf("# Covariance\n");  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     for(i=1;i<=npar;i++){  {
       /*  if (k>nlstate) k=1;    int i;
       i1=(i-1)/(ncovmodel*nlstate)+1;    int l=1, lmax=20;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    double k1,k2,k3,k4,res,fx;
       printf("%s%d%d",alph[k],i1,tab[i]);*/    double p2[MAXPARM+1];
       fprintf(ficres,"%3d",i);    int k;
       printf("%3d",i);  
       for(j=1; j<=i;j++){    fx=func(x);
         fprintf(ficres," %.5e",matcov[i][j]);    for (k=1; k<=2; k++) {
         printf(" %.5e",matcov[i][j]);      for (i=1;i<=npar;i++) p2[i]=x[i];
       }      p2[thetai]=x[thetai]+delti[thetai]/k;
       fprintf(ficres,"\n");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       printf("\n");      k1=func(p2)-fx;
       k++;    
     }      p2[thetai]=x[thetai]+delti[thetai]/k;
          p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     while((c=getc(ficpar))=='#' && c!= EOF){      k2=func(p2)-fx;
       ungetc(c,ficpar);    
       fgets(line, MAXLINE, ficpar);      p2[thetai]=x[thetai]-delti[thetai]/k;
       puts(line);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       fputs(line,ficparo);      k3=func(p2)-fx;
     }    
     ungetc(c,ficpar);      p2[thetai]=x[thetai]-delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      k4=func(p2)-fx;
          res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     if (fage <= 2) {  #ifdef DEBUG
       bage = agemin;      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);
       fage = agemax;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     }  #endif
        }
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    return res;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  }
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  
    /************** Inverse of matrix **************/
     while((c=getc(ficpar))=='#' && c!= EOF){  void ludcmp(double **a, int n, int *indx, double *d) 
     ungetc(c,ficpar);  { 
     fgets(line, MAXLINE, ficpar);    int i,imax,j,k; 
     puts(line);    double big,dum,sum,temp; 
     fputs(line,ficparo);    double *vv; 
   }   
   ungetc(c,ficpar);    vv=vector(1,n); 
      *d=1.0; 
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);    for (i=1;i<=n;i++) { 
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);      big=0.0; 
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);      for (j=1;j<=n;j++) 
              if ((temp=fabs(a[i][j])) > big) big=temp; 
   while((c=getc(ficpar))=='#' && c!= EOF){      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     ungetc(c,ficpar);      vv[i]=1.0/big; 
     fgets(line, MAXLINE, ficpar);    } 
     puts(line);    for (j=1;j<=n;j++) { 
     fputs(line,ficparo);      for (i=1;i<j;i++) { 
   }        sum=a[i][j]; 
   ungetc(c,ficpar);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
          a[i][j]=sum; 
       } 
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      big=0.0; 
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
   fscanf(ficpar,"pop_based=%d\n",&popbased);        for (k=1;k<j;k++) 
    fprintf(ficparo,"pop_based=%d\n",popbased);            sum -= a[i][k]*a[k][j]; 
    fprintf(ficres,"pop_based=%d\n",popbased);          a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
   while((c=getc(ficpar))=='#' && c!= EOF){          big=dum; 
     ungetc(c,ficpar);          imax=i; 
     fgets(line, MAXLINE, ficpar);        } 
     puts(line);      } 
     fputs(line,ficparo);      if (j != imax) { 
   }        for (k=1;k<=n;k++) { 
   ungetc(c,ficpar);          dum=a[imax][k]; 
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);          a[imax][k]=a[j][k]; 
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);          a[j][k]=dum; 
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);        } 
         *d = -(*d); 
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);        vv[imax]=vv[j]; 
       } 
          indx[j]=imax; 
     /*------------ gnuplot -------------*/      if (a[j][j] == 0.0) a[j][j]=TINY; 
     /*chdir(pathcd);*/      if (j != n) { 
     strcpy(optionfilegnuplot,optionfilefiname);        dum=1.0/(a[j][j]); 
     strcat(optionfilegnuplot,".plt");        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      } 
       printf("Problem with file %s",optionfilegnuplot);goto end;    } 
     }    free_vector(vv,1,n);  /* Doesn't work */
 #ifdef windows  ;
     fprintf(ficgp,"cd \"%s\" \n",pathc);  } 
 #endif  
 m=pow(2,cptcoveff);  void lubksb(double **a, int n, int *indx, double b[]) 
    { 
  /* 1eme*/    int i,ii=0,ip,j; 
   for (cpt=1; cpt<= nlstate ; cpt ++) {    double sum; 
    for (k1=1; k1<= m ; k1 ++) {   
     for (i=1;i<=n;i++) { 
 #ifdef windows      ip=indx[i]; 
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);      sum=b[ip]; 
 #endif      b[ip]=b[i]; 
 #ifdef unix      if (ii) 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
 #endif      else if (sum) ii=i; 
       b[i]=sum; 
 for (i=1; i<= nlstate ; i ++) {    } 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    for (i=n;i>=1;i--) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      sum=b[i]; 
 }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      b[i]=sum/a[i][i]; 
     for (i=1; i<= nlstate ; i ++) {    } 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }  void pstamp(FILE *fichier)
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  {
      for (i=1; i<= nlstate ; i ++) {    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    /************ Frequencies ********************/
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  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[])
 #ifdef unix  {  /* Some frequencies */
 fprintf(ficgp,"\nset ter gif small size 400,300");    
 #endif    int i, m, jk, j1, bool, z1,j;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    int first;
    }    double ***freq; /* Frequencies */
   }    double *pp, **prop;
   /*2 eme*/    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     char fileresp[FILENAMELENGTH];
   for (k1=1; k1<= m ; k1 ++) {    
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    pp=vector(1,nlstate);
        prop=matrix(1,nlstate,iagemin,iagemax+3);
     for (i=1; i<= nlstate+1 ; i ++) {    strcpy(fileresp,"p");
       k=2*i;    strcat(fileresp,fileres);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    if((ficresp=fopen(fileresp,"w"))==NULL) {
       for (j=1; j<= nlstate+1 ; j ++) {      printf("Problem with prevalence resultfile: %s\n", fileresp);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      exit(0);
 }      }
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    j1=0;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    
       for (j=1; j<= nlstate+1 ; j ++) {    j=cptcoveff;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      first=1;
       fprintf(ficgp,"\" t\"\" w l 0,");  
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
       for (j=1; j<= nlstate+1 ; j ++) {    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /*    j1++; */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
 }          /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          scanf("%d", i);*/
       else fprintf(ficgp,"\" t\"\" w l 0,");        for (i=-5; i<=nlstate+ndeath; i++)  
     }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            for(m=iagemin; m <= iagemax+3; m++)
   }              freq[i][jk][m]=0;
          
   /*3eme*/        for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
   for (k1=1; k1<= m ; k1 ++) {            prop[i][m]=0;
     for (cpt=1; cpt<= nlstate ; cpt ++) {        
       k=2+nlstate*(cpt-1);        dateintsum=0;
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);        k2cpt=0;
       for (i=1; i< nlstate ; i ++) {        for (i=1; i<=imx; i++) {
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          bool=1;
       }          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            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 */
                  bool=0;
   /* CV preval stat */                /* 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 (k1=1; k1<= m ; k1 ++) {                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
     for (cpt=1; cpt<nlstate ; cpt ++) {                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
       k=3;                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);              } 
       for (i=1; i< nlstate ; i ++)          }
         fprintf(ficgp,"+$%d",k+i+1);   
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          if (bool==1){
                  for(m=firstpass; m<=lastpass; m++){
       l=3+(nlstate+ndeath)*cpt;              k2=anint[m][i]+(mint[m][i]/12.);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       for (i=1; i< nlstate ; i ++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         l=3+(nlstate+ndeath)*cpt;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         fprintf(ficgp,"+$%d",l+i+1);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       }                if (m<lastpass) {
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     }                }
   }                  
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   /* proba elementaires */                  dateintsum=dateintsum+k2;
    for(i=1,jk=1; i <=nlstate; i++){                  k2cpt++;
     for(k=1; k <=(nlstate+ndeath); k++){                }
       if (k != i) {                /*}*/
         for(j=1; j <=ncovmodel; j++){            }
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/          }
           /*fprintf(ficgp,"%s",alph[1]);*/        } /* end i */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);         
           jk++;        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
           fprintf(ficgp,"\n");        pstamp(ficresp);
         }        if  (cptcovn>0) {
       }          fprintf(ficresp, "\n#********** Variable "); 
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficresp, "**********\n#");
           fprintf(ficlog, "\n#********** Variable "); 
   for(jk=1; jk <=m; jk++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);          fprintf(ficlog, "**********\n#");
    i=1;        }
    for(k2=1; k2<=nlstate; k2++) {        for(i=1; i<=nlstate;i++) 
      k3=i;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
      for(k=1; k<=(nlstate+ndeath); k++) {        fprintf(ficresp, "\n");
        if (k != k2){        
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        for(i=iagemin; i <= iagemax+3; i++){
 ij=1;          if(i==iagemax+3){
         for(j=3; j <=ncovmodel; j++) {            fprintf(ficlog,"Total");
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          }else{
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            if(first==1){
             ij++;              first=0;
           }              printf("See log file for details...\n");
           else            }
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            fprintf(ficlog,"Age %d", i);
         }          }
           fprintf(ficgp,")/(1");          for(jk=1; jk <=nlstate ; jk++){
                    for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         for(k1=1; k1 <=nlstate; k1++){                pp[jk] += freq[jk][m][i]; 
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          }
 ij=1;          for(jk=1; jk <=nlstate ; jk++){
           for(j=3; j <=ncovmodel; j++){            for(m=-1, pos=0; m <=0 ; m++)
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              pos += freq[jk][m][i];
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            if(pp[jk]>=1.e-10){
             ij++;              if(first==1){
           }                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           else              }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           }            }else{
           fprintf(ficgp,")");              if(first==1)
         }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            }
         i=i+ncovmodel;          }
        }  
      }          for(jk=1; jk <=nlstate ; jk++){
    }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);              pp[jk] += freq[jk][m][i];
   }          }       
              for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   fclose(ficgp);            pos += pp[jk];
   /* end gnuplot */            posprop += prop[jk][i];
              }
 chdir(path);          for(jk=1; jk <=nlstate ; jk++){
                if(pos>=1.e-5){
     free_ivector(wav,1,imx);              if(first==1)
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     free_ivector(num,1,n);            }else{
     free_vector(agedc,1,n);              if(first==1)
     /*free_matrix(covar,1,NCOVMAX,1,n);*/                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     fclose(ficparo);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     fclose(ficres);            }
     /*  }*/            if( i <= iagemax){
                  if(pos>=1.e-5){
    /*________fin mle=1_________*/                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                    /*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]);*/
                }
     /* No more information from the sample is required now */              else
   /* Reads comments: lines beginning with '#' */                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          
     puts(line);          for(jk=-1; jk <=nlstate+ndeath; jk++)
     fputs(line,ficparo);            for(m=-1; m <=nlstate+ndeath; m++)
   }              if(freq[jk][m][i] !=0 ) {
   ungetc(c,ficpar);              if(first==1)
                  printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);              }
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          if(i <= iagemax)
 /*--------- index.htm --------*/            fprintf(ficresp,"\n");
           if(first==1)
   strcpy(optionfilehtm,optionfile);            printf("Others in log...\n");
   strcat(optionfilehtm,".htm");          fprintf(ficlog,"\n");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        }
     printf("Problem with %s \n",optionfilehtm);goto end;        /*}*/
   }    }
     dateintmean=dateintsum/k2cpt; 
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">   
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    fclose(ficresp);
 Total number of observations=%d <br>    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    free_vector(pp,1,nlstate);
 <hr  size=\"2\" color=\"#EC5E5E\">    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
 <li>Outputs files<br><br>\n    /* End of Freq */
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  }
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>  /************ Prevalence ********************/
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>  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)
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>  {  
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>       in each health status at the date of interview (if between dateprev1 and dateprev2).
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>       We still use firstpass and lastpass as another selection.
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    */
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>   
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    int i, m, jk, j1, bool, z1,j;
   
  fprintf(fichtm," <li>Graphs</li><p>");    double **prop;
     double posprop; 
  m=cptcoveff;    double  y2; /* in fractional years */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    int iagemin, iagemax;
     int first; /** to stop verbosity which is redirected to log file */
  j1=0;  
  for(k1=1; k1<=m;k1++){    iagemin= (int) agemin;
    for(i1=1; i1<=ncodemax[k1];i1++){    iagemax= (int) agemax;
        j1++;    /*pp=vector(1,nlstate);*/
        if (cptcovn > 0) {    prop=matrix(1,nlstate,iagemin,iagemax+3); 
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
          for (cpt=1; cpt<=cptcoveff;cpt++)    j1=0;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);    
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    /*j=cptcoveff;*/
        }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        first=1;
        for(cpt=1; cpt<nlstate;cpt++){    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      /*for(i1=1; i1<=ncodemax[k1];i1++){
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        j1++;*/
        }        
     for(cpt=1; cpt<=nlstate;cpt++) {        for (i=1; i<=nlstate; i++)  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          for(m=iagemin; m <= iagemax+3; m++)
 interval) in state (%d): v%s%d%d.gif <br>            prop[i][m]=0.0;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);         
      }        for (i=1; i<=imx; i++) { /* Each individual */
      for(cpt=1; cpt<=nlstate;cpt++) {          bool=1;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          if  (cptcovn>0) {
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            for (z1=1; z1<=cptcoveff; z1++) 
      }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and                bool=0;
 health expectancies in states (1) and (2): e%s%d.gif<br>          } 
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          if (bool==1) { 
 fprintf(fichtm,"\n</body>");            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
    }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
  }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 fclose(fichtm);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
   /*--------------- Prevalence limit --------------*/                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                  if (s[m][i]>0 && s[m][i]<=nlstate) { 
   strcpy(filerespl,"pl");                  /*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]]);*/
   strcat(filerespl,fileres);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                  prop[s[m][i]][iagemax+3] += weight[i]; 
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                } 
   }              }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            } /* end selection of waves */
   fprintf(ficrespl,"#Prevalence limit\n");          }
   fprintf(ficrespl,"#Age ");        }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        for(i=iagemin; i <= iagemax+3; i++){  
   fprintf(ficrespl,"\n");          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
              posprop += prop[jk][i]; 
   prlim=matrix(1,nlstate,1,nlstate);          } 
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(jk=1; jk <=nlstate ; jk++){     
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            if( i <=  iagemax){ 
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              if(posprop>=1.e-5){ 
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                probs[i][jk][j1]= prop[jk][i]/posprop;
   k=0;              } else{
   agebase=agemin;                if(first==1){
   agelim=agemax;                  first=0;
   ftolpl=1.e-10;                  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]);
   i1=cptcoveff;                }
   if (cptcovn < 1){i1=1;}              }
             } 
   for(cptcov=1;cptcov<=i1;cptcov++){          }/* end jk */ 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }/* end i */ 
         k=k+1;      /*} *//* end i1 */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    } /* end j1 */
         fprintf(ficrespl,"\n#******");    
         for(j=1;j<=cptcoveff;j++)    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /*free_vector(pp,1,nlstate);*/
         fprintf(ficrespl,"******\n");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
          }  /* End of prevalence */
         for (age=agebase; age<=agelim; age++){  
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  /************* Waves Concatenation ***************/
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)  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)
           fprintf(ficrespl," %.5f", prlim[i][i]);  {
           fprintf(ficrespl,"\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
     }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   fclose(ficrespl);       and mw[mi+1][i]. dh depends on stepm.
        */
   /*------------- h Pij x at various ages ------------*/  
      int i, mi, m;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {       double sum=0., jmean=0.;*/
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    int first;
   }    int j, k=0,jk, ju, jl;
   printf("Computing pij: result on file '%s' \n", filerespij);    double sum=0.;
      first=0;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    jmin=100000;
   /*if (stepm<=24) stepsize=2;*/    jmax=-1;
     jmean=0.;
   agelim=AGESUP;    for(i=1; i<=imx; i++){
   hstepm=stepsize*YEARM; /* Every year of age */      mi=0;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      m=firstpass;
        while(s[m][i] <= nlstate){
   k=0;        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   for(cptcov=1;cptcov<=i1;cptcov++){          mw[++mi][i]=m;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        if(m >=lastpass)
       k=k+1;          break;
         fprintf(ficrespij,"\n#****** ");        else
         for(j=1;j<=cptcoveff;j++)          m++;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      }/* end while */
         fprintf(ficrespij,"******\n");      if (s[m][i] > nlstate){
                mi++;     /* Death is another wave */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        /* if(mi==0)  never been interviewed correctly before death */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */           /* Only death is a correct wave */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        mw[mi][i]=m;
           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);        wav[i]=mi;
           fprintf(ficrespij,"# Age");      if(mi==0){
           for(i=1; i<=nlstate;i++)        nbwarn++;
             for(j=1; j<=nlstate+ndeath;j++)        if(first==0){
               fprintf(ficrespij," %1d-%1d",i,j);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           fprintf(ficrespij,"\n");          first=1;
           for (h=0; h<=nhstepm; h++){        }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        if(first==1){
             for(i=1; i<=nlstate;i++)          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
               for(j=1; j<=nlstate+ndeath;j++)        }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      } /* end mi==0 */
             fprintf(ficrespij,"\n");    } /* End individuals */
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for(i=1; i<=imx; i++){
           fprintf(ficrespij,"\n");      for(mi=1; mi<wav[i];mi++){
         }        if (stepm <=0)
     }          dh[mi][i]=1;
   }        else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/            if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   fclose(ficrespij);              if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
   if(stepm == 1) {                nberr++;
   /*---------- Forecasting ------------------*/                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]);
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;                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("calage= %f", calagedate);*/                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);
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              }
               k=k+1;
               if (j >= jmax){
   strcpy(fileresf,"f");                jmax=j;
   strcat(fileresf,fileres);                ijmax=i;
   if((ficresf=fopen(fileresf,"w"))==NULL) {              }
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;              if (j <= jmin){
   }                jmin=j;
   printf("Computing forecasting: result on file '%s' \n", fileresf);                ijmin=i;
               }
   free_matrix(mint,1,maxwav,1,n);              sum=sum+j;
   free_matrix(anint,1,maxwav,1,n);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   free_matrix(agev,1,maxwav,1,imx);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   /* Mobile average */            }
           }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   if (mobilav==1) {  /*        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]); */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)            k=k+1;
       for (i=1; i<=nlstate;i++)            if (j >= jmax) {
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)              jmax=j;
           mobaverage[(int)agedeb][i][cptcod]=0.;              ijmax=i;
                }
     for (agedeb=bage+4; agedeb<=fage; agedeb++){            else if (j <= jmin){
       for (i=1; i<=nlstate;i++){              jmin=j;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              ijmin=i;
           for (cpt=0;cpt<=4;cpt++){            }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           }            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;            if(j<0){
         }              nberr++;
       }              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     }                fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   }            }
             sum=sum+j;
   stepsize=(int) (stepm+YEARM-1)/YEARM;          }
   if (stepm<=12) stepsize=1;          jk= j/stepm;
           jl= j -jk*stepm;
   agelim=AGESUP;          ju= j -(jk+1)*stepm;
   /*hstepm=stepsize*YEARM; *//* Every year of age */          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   hstepm=1;            if(jl==0){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */              dh[mi][i]=jk;
   yp1=modf(dateintmean,&yp);              bh[mi][i]=0;
   anprojmean=yp;            }else{ /* We want a negative bias in order to only have interpolation ie
   yp2=modf((yp1*12),&yp);                    * to avoid the price of an extra matrix product in likelihood */
   mprojmean=yp;              dh[mi][i]=jk+1;
   yp1=modf((yp2*30.5),&yp);              bh[mi][i]=ju;
   jprojmean=yp;            }
   if(jprojmean==0) jprojmean=1;          }else{
   if(mprojmean==0) jprojmean=1;            if(jl <= -ju){
               dh[mi][i]=jk;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);              bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
   if (popforecast==1) {                                   */
     if((ficpop=fopen(popfile,"r"))==NULL)    {            }
       printf("Problem with population file : %s\n",popfile);goto end;            else{
     }              dh[mi][i]=jk+1;
     popage=ivector(0,AGESUP);              bh[mi][i]=ju;
     popeffectif=vector(0,AGESUP);            }
     popcount=vector(0,AGESUP);            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
     i=1;                bh[mi][i]=ju; /* At least one step */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)              /*  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);*/
       {            }
         i=i+1;          } /* end if mle */
       }        }
     imx=i;      } /* end wave */
        }
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    jmean=sum/k;
   }    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
     fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
   for(cptcov=1;cptcov<=i1;cptcov++){   }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;  /*********** Tricode ****************************/
       fprintf(ficresf,"\n#******");  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
       for(j=1;j<=cptcoveff;j++) {  {
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
       }    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
       fprintf(ficresf,"******\n");     * Boring subroutine which should only output nbcode[Tvar[j]][k]
       fprintf(ficresf,"# StartingAge FinalAge");     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);     * nbcode[Tvar[j]][1]= 
       if (popforecast==1)  fprintf(ficresf," [Population]");    */
      
       for (cpt=0; cpt<4;cpt++) {    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
         fprintf(ficresf,"\n");    int modmaxcovj=0; /* Modality max of covariates j */
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      int cptcode=0; /* Modality max of covariates j */
     int modmincovj=0; /* Modality min of covariates j */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */  
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
         nhstepm = nhstepm/hstepm;    cptcoveff=0; 
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/   
     for (k=-1; k < maxncov; k++) Ndum[k]=0;
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
         oldm=oldms;savm=savms;  
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /* 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 (h=0; h<=nhstepm; h++){      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
           if (h==(int) (calagedate+YEARM*cpt)) {                                 modality of this covariate Vj*/ 
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
           }                                      * If product of Vn*Vm, still boolean *:
           for(j=1; j<=nlstate+ndeath;j++) {                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
             kk1=0.;kk2=0;                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
             for(i=1; i<=nlstate;i++) {                /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
               if (mobilav==1)                                        modality of the nth covariate of individual i. */
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        if (ij > modmaxcovj)
               else {          modmaxcovj=ij; 
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        else if (ij < modmincovj) 
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/          modmincovj=ij; 
               }        if ((ij < -1) && (ij > NCOVMAX)){
           printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];          exit(1);
             }        }else
                  Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
             if (h==(int)(calagedate+12*cpt)){        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
               fprintf(ficresf," %.3f", kk1);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                      /* getting the maximum value of the modality of the covariate
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
             }           female is 1, then modmaxcovj=1.*/
           }      }
         }      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      cptcode=modmaxcovj;
       }      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
       }     /*for (i=0; i<=cptcode; i++) {*/
     }      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
   }        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
   if (popforecast==1) {          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
     free_ivector(popage,0,AGESUP);        }
     free_vector(popeffectif,0,AGESUP);        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
     free_vector(popcount,0,AGESUP);           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
   }      } /* Ndum[-1] number of undefined modalities */
   free_imatrix(s,1,maxwav+1,1,n);  
   free_vector(weight,1,n);      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
   fclose(ficresf);      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
   }/* End forecasting */      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
   else{         modmincovj=3; modmaxcovj = 7;
     erreur=108;         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
   }         variables V1_1 and V1_2.
          nbcode[Tvar[j]][ij]=k;
   /*---------- Health expectancies and variances ------------*/         nbcode[Tvar[j]][1]=0;
          nbcode[Tvar[j]][2]=1;
   strcpy(filerest,"t");         nbcode[Tvar[j]][3]=2;
   strcat(filerest,fileres);      */
   if((ficrest=fopen(filerest,"w"))==NULL) {      ij=1; /* ij is similar to i but can jumps over null modalities */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
   }        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          /*recode from 0 */
           if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
             nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
   strcpy(filerese,"e");                                       k is a modality. If we have model=V1+V1*sex 
   strcat(filerese,fileres);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   if((ficreseij=fopen(filerese,"w"))==NULL) {            ij++;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          }
   }          if (ij > ncodemax[j]) break; 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        }  /* end of loop on */
       } /* end of loop on modality */ 
  strcpy(fileresv,"v");    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   strcat(fileresv,fileres);    
   if((ficresvij=fopen(fileresv,"w"))==NULL) {   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    
   }    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);     /* 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 */ 
   k=0;     Ndum[ij]++; 
   for(cptcov=1;cptcov<=i1;cptcov++){   } 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;   ij=1;
       fprintf(ficrest,"\n#****** ");   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
       for(j=1;j<=cptcoveff;j++)     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     if((Ndum[i]!=0) && (i<=ncovcol)){
       fprintf(ficrest,"******\n");       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
        Tvaraff[ij]=i; /*For printing (unclear) */
       fprintf(ficreseij,"\n#****** ");       ij++;
       for(j=1;j<=cptcoveff;j++)     }else
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);         Tvaraff[ij]=0;
       fprintf(ficreseij,"******\n");   }
    ij--;
       fprintf(ficresvij,"\n#****** ");   cptcoveff=ij; /*Number of total covariates*/
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  }
       fprintf(ficresvij,"******\n");  
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  /*********** Health Expectancies ****************/
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;  {
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    /* Health expectancies, no variances */
          int i, j, nhstepm, hstepm, h, nstepm;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    int nhstepma, nstepma; /* Decreasing with age */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    double age, agelim, hf;
       fprintf(ficrest,"\n");    double ***p3mat;
            double eip;
       hf=1;  
       if (stepm >= YEARM) hf=stepm/YEARM;    pstamp(ficreseij);
       epj=vector(1,nlstate+1);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
       for(age=bage; age <=fage ;age++){    fprintf(ficreseij,"# Age");
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    for(i=1; i<=nlstate;i++){
         if (popbased==1) {      for(j=1; j<=nlstate;j++){
           for(i=1; i<=nlstate;i++)        fprintf(ficreseij," e%1d%1d ",i,j);
             prlim[i][i]=probs[(int)age][i][k];      }
         }      fprintf(ficreseij," e%1d. ",i);
            }
         fprintf(ficrest," %.0f",age);    fprintf(ficreseij,"\n");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    if(estepm < stepm){
           }      printf ("Problem %d lower than %d\n",estepm, stepm);
           epj[nlstate+1] +=epj[j];    }
         }    else  hstepm=estepm;   
         for(i=1, vepp=0.;i <=nlstate;i++)    /* We compute the life expectancy from trapezoids spaced every estepm months
           for(j=1;j <=nlstate;j++)     * This is mainly to measure the difference between two models: for example
             vepp += vareij[i][j][(int)age];     * if stepm=24 months pijx are given only every 2 years and by summing them
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));     * we are calculating an estimate of the Life Expectancy assuming a linear 
         for(j=1;j <=nlstate;j++){     * progression in between and thus overestimating or underestimating according
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));     * 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
         fprintf(ficrest,"\n");     * to compare the new estimate of Life expectancy with the same linear 
       }     * hypothesis. A more precise result, taking into account a more precise
     }     * curvature will be obtained if estepm is as small as stepm. */
   }  
            /* For example we decided to compute the life expectancy with the smallest unit */
            /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
  fclose(ficreseij);       Look at hpijx to understand the reason of that which relies in memory size
  fclose(ficresvij);       and note for a fixed period like estepm months */
   fclose(ficrest);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   fclose(ficpar);       survival function given by stepm (the optimization length). Unfortunately it
   free_vector(epj,1,nlstate+1);       means that if the survival funtion is printed only each two years of age and if
   /*  scanf("%d ",i); */       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.
   /*------- Variance limit prevalence------*/      */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 strcpy(fileresvpl,"vpl");  
   strcat(fileresvpl,fileres);    agelim=AGESUP;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    /* If stepm=6 months */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     exit(0);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   }      
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
  k=0;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
  for(cptcov=1;cptcov<=i1;cptcov++){    /* if (stepm >= YEARM) hstepm=1;*/
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      k=k+1;    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      fprintf(ficresvpl,"\n#****** ");  
      for(j=1;j<=cptcoveff;j++)    for (age=bage; age<=fage; age ++){ 
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
      fprintf(ficresvpl,"******\n");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
            /* if (stepm >= YEARM) hstepm=1;*/
      varpl=matrix(1,nlstate,(int) bage, (int) fage);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
      oldm=oldms;savm=savms;  
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,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 */
       
   fclose(ficresvpl);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
   /*---------- End : free ----------------*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      
        printf("%d|",(int)age);fflush(stdout);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      
        /* Computing expectancies */
        for(i=1; i<=nlstate;i++)
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        for(j=1; j<=nlstate;j++)
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);            
              /* 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]);*/
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);          }
    
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
   if(erreur >0)        eip=0;
     printf("End of Imach with error %d\n",erreur);        for(j=1; j<=nlstate;j++){
   else   printf("End of Imach\n");          eip +=eij[i][j][(int)age];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
          }
   /* 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);*/        fprintf(ficreseij,"%9.4f", eip );
   /*printf("Total time was %d uSec.\n", total_usecs);*/      }
   /*------ End -----------*/      fprintf(ficreseij,"\n");
       
     }
  end:    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 #ifdef windows    printf("\n");
   /* chdir(pathcd);*/    fprintf(ficlog,"\n");
 #endif    
  /*system("wgnuplot graph.plt");*/  }
  /*system("../gp37mgw/wgnuplot graph.plt");*/  
  /*system("cd ../gp37mgw");*/  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[] )
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);  {
  strcat(plotcmd," ");    /* Covariances of health expectancies eij and of total life expectancies according
  strcat(plotcmd,optionfilegnuplot);     to initial status i, ei. .
  system(plotcmd);    */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
 #ifdef windows    int nhstepma, nstepma; /* Decreasing with age */
   while (z[0] != 'q') {    double age, agelim, hf;
     chdir(path);    double ***p3matp, ***p3matm, ***varhe;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    double **dnewm,**doldm;
     scanf("%s",z);    double *xp, *xm;
     if (z[0] == 'c') system("./imach");    double **gp, **gm;
     else if (z[0] == 'e') {    double ***gradg, ***trgradg;
       chdir(path);    int theta;
       system(optionfilehtm);  
     }    double eip, vip;
     else if (z[0] == 'q') exit(0);  
   }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
 #endif    xp=vector(1,npar);
 }    xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
     pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
     }
     fprintf(ficresstdeij,"\n");
   
     pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
         for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
       }
     fprintf(ficrescveij,"\n");
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
           }
         }
        
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       
   
        for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
   
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
     
     int movingaverage();
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  k1, l1, tj;
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } */ /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else        fprintf(ficgp," %%*lf (%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
   #if defined(__GNUC__) 
   #include <gnu/libc-version.h>  /* Only on gnu */
   struct utsname sysInfo;
   #endif
   
   #include <stdint.h>
      int cross = CROSS;
      if (cross){
        printf("Cross-");
        fprintf(ficlog,"Cross-");
      }
      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");
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version()); 
   
   #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");
              frintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo();
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.22  
changed lines
  Added in v.1.176


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