Diff for /imach/src/imach.c between versions 1.29 and 1.185

version 1.29, 2002/03/06 19:02:50 version 1.185, 2015/03/11 13:26:42
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.185  2015/03/11 13:26:42  brouard
      Summary: Inclusion of compile and links command line for Intel Compiler
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.184  2015/03/11 11:52:39  brouard
   first survey ("cross") where individuals from different ages are    Summary: Back from Windows 8. Intel Compiler
   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 1.183  2015/03/10 20:34:32  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: 0.98q0, trying with directest, mnbrak fixed
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    We use directest instead of original Powell test; probably no
   model. More health states you consider, more time is necessary to reach the    incidence on the results, but better justifications;
   Maximum Likelihood of the parameters involved in the model.  The    We fixed Numerical Recipes mnbrak routine which was wrong and gave
   simplest model is the multinomial logistic model where pij is the    wrong results.
   probabibility to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.182  2015/02/12 08:19:57  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Summary: Trying to keep directest which seems simpler and more general
   'age' is age and 'sex' is a covariate. If you want to have a more    Author: Nicolas Brouard
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.181  2015/02/11 23:22:24  brouard
   you to do it.  More covariates you add, slower the    Summary: Comments on Powell added
   convergence.  
     Author:
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.180  2015/02/11 17:33:45  brouard
   identical for each individual. Also, if a individual missed an    Summary: Finishing move from main to function (hpijx and prevalence_limit)
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.179  2015/01/04 09:57:06  brouard
     Summary: back to OS/X
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.178  2015/01/04 09:35:48  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    *** empty log message ***
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.177  2015/01/03 18:40:56  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    Summary: Still testing ilc32 on OSX
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.176  2015/01/03 16:45:04  brouard
     *** empty log message ***
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.175  2015/01/03 16:33:42  brouard
      *** empty log message ***
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.174  2015/01/03 16:15:49  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: Still in cross-compilation
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.173  2015/01/03 12:06:26  brouard
   software can be distributed freely for non commercial use. Latest version    Summary: trying to detect cross-compilation
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.172  2014/12/27 12:07:47  brouard
      Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
 #include <math.h>  
 #include <stdio.h>    Revision 1.171  2014/12/23 13:26:59  brouard
 #include <stdlib.h>    Summary: Back from Visual C
 #include <unistd.h>  
     Still problem with utsname.h on Windows
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Revision 1.170  2014/12/23 11:17:12  brouard
 #define FILENAMELENGTH 80    Summary: Cleaning some \%% back to %%
 /*#define DEBUG*/  
 #define windows    The escape was mandatory for a specific compiler (which one?), but too many warnings.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.169  2014/12/22 23:08:31  brouard
     Summary: 0.98p
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Outputs some informations on compiler used, OS etc. Testing on different platforms.
   
 #define NINTERVMAX 8    Revision 1.168  2014/12/22 15:17:42  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Summary: update
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.167  2014/12/22 13:50:56  brouard
 #define MAXN 20000    Summary: Testing uname and compiler version and if compiled 32 or 64
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Testing on Linux 64
 #define AGEBASE 40  
     Revision 1.166  2014/12/22 11:40:47  brouard
     *** empty log message ***
 int erreur; /* Error number */  
 int nvar;    Revision 1.165  2014/12/16 11:20:36  brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Summary: After compiling on Visual C
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    * imach.c (Module): Merging 1.61 to 1.162
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.164  2014/12/16 10:52:11  brouard
 int popbased=0;    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
   
 int *wav; /* Number of waves for this individuual 0 is possible */    * imach.c (Module): Merging 1.61 to 1.162
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.163  2014/12/16 10:30:11  brouard
 int mle, weightopt;    * imach.c (Module): Merging 1.61 to 1.162
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.162  2014/09/25 11:43:39  brouard
 double jmean; /* Mean space between 2 waves */    Summary: temporary backup 0.99!
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.1  2014/09/16 11:06:58  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Summary: With some code (wrong) for nlopt
 FILE *ficgp,*ficresprob,*ficpop;  
 FILE *ficreseij;    Author:
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.161  2014/09/15 20:41:41  brouard
   char fileresv[FILENAMELENGTH];    Summary: Problem with macro SQR on Intel compiler
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.160  2014/09/02 09:24:05  brouard
     *** empty log message ***
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.159  2014/09/01 10:34:10  brouard
 #define FTOL 1.0e-10    Summary: WIN32
     Author: Brouard
 #define NRANSI  
 #define ITMAX 200    Revision 1.158  2014/08/27 17:11:51  brouard
     *** empty log message ***
 #define TOL 2.0e-4  
     Revision 1.157  2014/08/27 16:26:55  brouard
 #define CGOLD 0.3819660    Summary: Preparing windows Visual studio version
 #define ZEPS 1.0e-10    Author: Brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     In order to compile on Visual studio, time.h is now correct and time_t
 #define GOLD 1.618034    and tm struct should be used. difftime should be used but sometimes I
 #define GLIMIT 100.0    just make the differences in raw time format (time(&now).
 #define TINY 1.0e-20    Trying to suppress #ifdef LINUX
     Add xdg-open for __linux in order to open default browser.
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.156  2014/08/25 20:10:10  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    *** empty log message ***
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.155  2014/08/25 18:32:34  brouard
 #define rint(a) floor(a+0.5)    Summary: New compile, minor changes
     Author: Brouard
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.154  2014/06/20 17:32:08  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Summary: Outputs now all graphs of convergence to period prevalence
   
 int imx;    Revision 1.153  2014/06/20 16:45:46  brouard
 int stepm;    Summary: If 3 live state, convergence to period prevalence on same graph
 /* Stepm, step in month: minimum step interpolation*/    Author: Brouard
   
 int m,nb;    Revision 1.152  2014/06/18 17:54:09  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.151  2014/06/18 16:43:30  brouard
 double dateintmean=0;    *** empty log message ***
   
 double *weight;    Revision 1.150  2014/06/18 16:42:35  brouard
 int **s; /* Status */    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 double *agedc, **covar, idx;    Author: brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.149  2014/06/18 15:51:14  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Summary: Some fixes in parameter files errors
 double ftolhess; /* Tolerance for computing hessian */    Author: Nicolas Brouard
   
 /**************** split *************************/    Revision 1.148  2014/06/17 17:38:48  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Summary: Nothing new
 {    Author: Brouard
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Just a new packaging for OS/X version 0.98nS
   
    l1 = strlen( path );                 /* length of path */    Revision 1.147  2014/06/16 10:33:11  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    *** empty log message ***
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.146  2014/06/16 10:20:28  brouard
 #else    Summary: Merge
    s = strrchr( path, '/' );            /* find last / */    Author: Brouard
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */    Merge, before building revised version.
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Revision 1.145  2014/06/10 21:23:15  brouard
     Summary: Debugging with valgrind
       if ( getwd( dirc ) == NULL ) {    Author: Nicolas Brouard
 #else  
       extern char       *getcwd( );    Lot of changes in order to output the results with some covariates
     After the Edimburgh REVES conference 2014, it seems mandatory to
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    improve the code.
 #endif    No more memory valgrind error but a lot has to be done in order to
          return( GLOCK_ERROR_GETCWD );    continue the work of splitting the code into subroutines.
       }    Also, decodemodel has been improved. Tricode is still not
       strcpy( name, path );             /* we've got it */    optimal. nbcode should be improved. Documentation has been added in
    } else {                             /* strip direcotry from path */    the source code.
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Revision 1.143  2014/01/26 09:45:38  brouard
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
       dirc[l1-l2] = 0;                  /* add zero */    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
    }  
    l1 = strlen( dirc );                 /* length of directory */    Revision 1.142  2014/01/26 03:57:36  brouard
 #ifdef windows    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.141  2014/01/26 02:42:01  brouard
    s = strrchr( name, '.' );            /* find last / */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.140  2011/09/02 10:37:54  brouard
    l1= strlen( name);    Summary: times.h is ok with mingw32 now.
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    Revision 1.139  2010/06/14 07:50:17  brouard
    finame[l1-l2]= 0;    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
    return( 0 );                         /* we're done */    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 }  
     Revision 1.138  2010/04/30 18:19:40  brouard
     *** empty log message ***
 /******************************************/  
     Revision 1.137  2010/04/29 18:11:38  brouard
 void replace(char *s, char*t)    (Module): Checking covariates for more complex models
 {    than V1+V2. A lot of change to be done. Unstable.
   int i;  
   int lg=20;    Revision 1.136  2010/04/26 20:30:53  brouard
   i=0;    (Module): merging some libgsl code. Fixing computation
   lg=strlen(t);    of likelione (using inter/intrapolation if mle = 0) in order to
   for(i=0; i<= lg; i++) {    get same likelihood as if mle=1.
     (s[i] = t[i]);    Some cleaning of code and comments added.
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.135  2009/10/29 15:33:14  brouard
 }    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
 int nbocc(char *s, char occ)    Revision 1.134  2009/10/29 13:18:53  brouard
 {    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   int i,j=0;  
   int lg=20;    Revision 1.133  2009/07/06 10:21:25  brouard
   i=0;    just nforces
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.132  2009/07/06 08:22:05  brouard
   if  (s[i] == occ ) j++;    Many tings
   }  
   return j;    Revision 1.131  2009/06/20 16:22:47  brouard
 }    Some dimensions resccaled
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.130  2009/05/26 06:44:34  brouard
 {    (Module): Max Covariate is now set to 20 instead of 8. A
   int i,lg,j,p=0;    lot of cleaning with variables initialized to 0. Trying to make
   i=0;    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    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
   
   lg=strlen(t);    Revision 1.128  2006/06/30 13:02:05  brouard
   for(j=0; j<p; j++) {    (Module): Clarifications on computing e.j
     (u[j] = t[j]);  
   }    Revision 1.127  2006/04/28 18:11:50  brouard
      u[p]='\0';    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
    for(j=0; j<= lg; j++) {    loop. Now we define nhstepma in the age loop.
     if (j>=(p+1))(v[j-p-1] = t[j]);    (Module): In order to speed up (in case of numerous covariates) we
   }    compute health expectancies (without variances) in a first step
 }    and then all the health expectancies with variances or standard
     deviation (needs data from the Hessian matrices) which slows the
 /********************** nrerror ********************/    computation.
     In the future we should be able to stop the program is only health
 void nrerror(char error_text[])    expectancies and graph are needed without standard deviations.
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.126  2006/04/28 17:23:28  brouard
   fprintf(stderr,"%s\n",error_text);    (Module): Yes the sum of survivors was wrong since
   exit(1);    imach-114 because nhstepm was no more computed in the age
 }    loop. Now we define nhstepma in the age loop.
 /*********************** vector *******************/    Version 0.98h
 double *vector(int nl, int nh)  
 {    Revision 1.125  2006/04/04 15:20:31  lievre
   double *v;    Errors in calculation of health expectancies. Age was not initialized.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Forecasting file added.
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.124  2006/03/22 17:13:53  lievre
 }    Parameters are printed with %lf instead of %f (more numbers after the comma).
     The log-likelihood is printed in the log file
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.123  2006/03/20 10:52:43  brouard
 {    * imach.c (Module): <title> changed, corresponds to .htm file
   free((FREE_ARG)(v+nl-NR_END));    name. <head> headers where missing.
 }  
     * imach.c (Module): Weights can have a decimal point as for
 /************************ivector *******************************/    English (a comma might work with a correct LC_NUMERIC environment,
 int *ivector(long nl,long nh)    otherwise the weight is truncated).
 {    Modification of warning when the covariates values are not 0 or
   int *v;    1.
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Version 0.98g
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;    Revision 1.122  2006/03/20 09:45:41  brouard
 }    (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 /******************free ivector **************************/    otherwise the weight is truncated).
 void free_ivector(int *v, long nl, long nh)    Modification of warning when the covariates values are not 0 or
 {    1.
   free((FREE_ARG)(v+nl-NR_END));    Version 0.98g
 }  
     Revision 1.121  2006/03/16 17:45:01  lievre
 /******************* imatrix *******************************/    * imach.c (Module): Comments concerning covariates added
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    * imach.c (Module): refinements in the computation of lli if
 {    status=-2 in order to have more reliable computation if stepm is
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    not 1 month. Version 0.98f
   int **m;  
      Revision 1.120  2006/03/16 15:10:38  lievre
   /* allocate pointers to rows */    (Module): refinements in the computation of lli if
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    status=-2 in order to have more reliable computation if stepm is
   if (!m) nrerror("allocation failure 1 in matrix()");    not 1 month. Version 0.98f
   m += NR_END;  
   m -= nrl;    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
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Revision 1.118  2006/03/14 18:20:07  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): varevsij Comments added explaining the second
   m[nrl] += NR_END;    table of variances if popbased=1 .
   m[nrl] -= ncl;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
      (Module): Function pstamp added
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    (Module): Version 0.98d
    
   /* return pointer to array of pointers to rows */    Revision 1.117  2006/03/14 17:16:22  brouard
   return m;    (Module): varevsij Comments added explaining the second
 }    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 /****************** free_imatrix *************************/    (Module): Function pstamp added
 void free_imatrix(m,nrl,nrh,ncl,nch)    (Module): Version 0.98d
       int **m;  
       long nch,ncl,nrh,nrl;    Revision 1.116  2006/03/06 10:29:27  brouard
      /* free an int matrix allocated by imatrix() */    (Module): Variance-covariance wrong links and
 {    varian-covariance of ej. is needed (Saito).
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Revision 1.115  2006/02/27 12:17:45  brouard
 }    (Module): One freematrix added in mlikeli! 0.98c
   
 /******************* matrix *******************************/    Revision 1.114  2006/02/26 12:57:58  brouard
 double **matrix(long nrl, long nrh, long ncl, long nch)    (Module): Some improvements in processing parameter
 {    filename with strsep.
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.113  2006/02/24 14:20:24  brouard
     (Module): Memory leaks checks with valgrind and:
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    datafile was not closed, some imatrix were not freed and on matrix
   if (!m) nrerror("allocation failure 1 in matrix()");    allocation too.
   m += NR_END;  
   m -= nrl;    Revision 1.112  2006/01/30 09:55:26  brouard
     (Module): Back to gnuplot.exe instead of wgnuplot.exe
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.111  2006/01/25 20:38:18  brouard
   m[nrl] += NR_END;    (Module): Lots of cleaning and bugs added (Gompertz)
   m[nrl] -= ncl;    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;    Revision 1.110  2006/01/25 00:51:50  brouard
 }    (Module): Lots of cleaning and bugs added (Gompertz)
   
 /*************************free matrix ************************/    Revision 1.109  2006/01/24 19:37:15  brouard
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    (Module): Comments (lines starting with a #) are allowed in data.
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Revision 1.108  2006/01/19 18:05:42  lievre
   free((FREE_ARG)(m+nrl-NR_END));    Gnuplot problem appeared...
 }    To be fixed
   
 /******************* ma3x *******************************/    Revision 1.107  2006/01/19 16:20:37  brouard
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Test existence of gnuplot in imach path
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Revision 1.106  2006/01/19 13:24:36  brouard
   double ***m;    Some cleaning and links added in html output
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.105  2006/01/05 20:23:19  lievre
   if (!m) nrerror("allocation failure 1 in matrix()");    *** empty log message ***
   m += NR_END;  
   m -= nrl;    Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): If the status is missing at the last wave but we know
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    that the person is alive, then we can code his/her status as -2
   m[nrl] += NR_END;    (instead of missing=-1 in earlier versions) and his/her
   m[nrl] -= ncl;    contributions to the likelihood is 1 - Prob of dying from last
     health status (= 1-p13= p11+p12 in the easiest case of somebody in
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    the healthy state at last known wave). Version is 0.98
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Revision 1.103  2005/09/30 15:54:49  lievre
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    (Module): sump fixed, loop imx fixed, and simplifications.
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;    Revision 1.102  2004/09/15 17:31:30  brouard
   for (j=ncl+1; j<=nch; j++)    Add the possibility to read data file including tab characters.
     m[nrl][j]=m[nrl][j-1]+nlay;  
      Revision 1.101  2004/09/15 10:38:38  brouard
   for (i=nrl+1; i<=nrh; i++) {    Fix on curr_time
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    Revision 1.100  2004/07/12 18:29:06  brouard
       m[i][j]=m[i][j-1]+nlay;    Add version for Mac OS X. Just define UNIX in Makefile
   }  
   return m;    Revision 1.99  2004/06/05 08:57:40  brouard
 }    *** empty log message ***
   
 /*************************free ma3x ************************/    Revision 1.98  2004/05/16 15:05:56  brouard
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    New version 0.97 . First attempt to estimate force of mortality
 {    directly from the data i.e. without the need of knowing the health
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    state at each age, but using a Gompertz model: log u =a + b*age .
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    This is the basic analysis of mortality and should be done before any
   free((FREE_ARG)(m+nrl-NR_END));    other analysis, in order to test if the mortality estimated from the
 }    cross-longitudinal survey is different from the mortality estimated
     from other sources like vital statistic data.
 /***************** f1dim *************************/  
 extern int ncom;    The same imach parameter file can be used but the option for mle should be -3.
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);    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.
 double f1dim(double x)  
 {    The output is very simple: only an estimate of the intercept and of
   int j;    the slope with 95% confident intervals.
   double f;  
   double *xt;    Current limitations:
      A) Even if you enter covariates, i.e. with the
   xt=vector(1,ncom);    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    B) There is no computation of Life Expectancy nor Life Table.
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);    Revision 1.97  2004/02/20 13:25:42  lievre
   return f;    Version 0.96d. Population forecasting command line is (temporarily)
 }    suppressed.
   
 /*****************brent *************************/    Revision 1.96  2003/07/15 15:38:55  brouard
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 {    rewritten within the same printf. Workaround: many printfs.
   int iter;  
   double a,b,d,etemp;    Revision 1.95  2003/07/08 07:54:34  brouard
   double fu,fv,fw,fx;    * imach.c (Repository):
   double ftemp;    (Repository): Using imachwizard code to output a more meaningful covariance
   double p,q,r,tol1,tol2,u,v,w,x,xm;    matrix (cov(a12,c31) instead of numbers.
   double e=0.0;  
      Revision 1.94  2003/06/27 13:00:02  brouard
   a=(ax < cx ? ax : cx);    Just cleaning
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    Revision 1.93  2003/06/25 16:33:55  brouard
   fw=fv=fx=(*f)(x);    (Module): On windows (cygwin) function asctime_r doesn't
   for (iter=1;iter<=ITMAX;iter++) {    exist so I changed back to asctime which exists.
     xm=0.5*(a+b);    (Module): Version 0.96b
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    Revision 1.92  2003/06/25 16:30:45  brouard
     printf(".");fflush(stdout);    (Module): On windows (cygwin) function asctime_r doesn't
 #ifdef DEBUG    exist so I changed back to asctime which exists.
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    Revision 1.91  2003/06/25 15:30:29  brouard
 #endif    * imach.c (Repository): Duplicated warning errors corrected.
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    (Repository): Elapsed time after each iteration is now output. It
       *xmin=x;    helps to forecast when convergence will be reached. Elapsed time
       return fx;    is stamped in powell.  We created a new html file for the graphs
     }    concerning matrix of covariance. It has extension -cov.htm.
     ftemp=fu;  
     if (fabs(e) > tol1) {    Revision 1.90  2003/06/24 12:34:15  brouard
       r=(x-w)*(fx-fv);    (Module): Some bugs corrected for windows. Also, when
       q=(x-v)*(fx-fw);    mle=-1 a template is output in file "or"mypar.txt with the design
       p=(x-v)*q-(x-w)*r;    of the covariance matrix to be input.
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;    Revision 1.89  2003/06/24 12:30:52  brouard
       q=fabs(q);    (Module): Some bugs corrected for windows. Also, when
       etemp=e;    mle=-1 a template is output in file "or"mypar.txt with the design
       e=d;    of the covariance matrix to be input.
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    Revision 1.88  2003/06/23 17:54:56  brouard
       else {    * 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.
         d=p/q;  
         u=x+d;    Revision 1.87  2003/06/18 12:26:01  brouard
         if (u-a < tol2 || b-u < tol2)    Version 0.96
           d=SIGN(tol1,xm-x);  
       }    Revision 1.86  2003/06/17 20:04:08  brouard
     } else {    (Module): Change position of html and gnuplot routines and added
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    routine fileappend.
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    Revision 1.85  2003/06/17 13:12:43  brouard
     fu=(*f)(u);    * imach.c (Repository): Check when date of death was earlier that
     if (fu <= fx) {    current date of interview. It may happen when the death was just
       if (u >= x) a=x; else b=x;    prior to the death. In this case, dh was negative and likelihood
       SHFT(v,w,x,u)    was wrong (infinity). We still send an "Error" but patch by
         SHFT(fv,fw,fx,fu)    assuming that the date of death was just one stepm after the
         } else {    interview.
           if (u < x) a=u; else b=u;    (Repository): Because some people have very long ID (first column)
           if (fu <= fw || w == x) {    we changed int to long in num[] and we added a new lvector for
             v=w;    memory allocation. But we also truncated to 8 characters (left
             w=u;    truncation)
             fv=fw;    (Repository): No more line truncation errors.
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {    Revision 1.84  2003/06/13 21:44:43  brouard
             v=u;    * imach.c (Repository): Replace "freqsummary" at a correct
             fv=fu;    place. It differs from routine "prevalence" which may be called
           }    many times. Probs is memory consuming and must be used with
         }    parcimony.
   }    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   nrerror("Too many iterations in brent");  
   *xmin=x;    Revision 1.83  2003/06/10 13:39:11  lievre
   return fx;    *** empty log message ***
 }  
     Revision 1.82  2003/06/05 15:57:20  brouard
 /****************** mnbrak ***********************/    Add log in  imach.c and  fullversion number is now printed.
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  */
             double (*func)(double))  /*
 {     Interpolated Markov Chain
   double ulim,u,r,q, dum;  
   double fu;    Short summary of the programme:
      
   *fa=(*func)(*ax);    This program computes Healthy Life Expectancies from
   *fb=(*func)(*bx);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   if (*fb > *fa) {    first survey ("cross") where individuals from different ages are
     SHFT(dum,*ax,*bx,dum)    interviewed on their health status or degree of disability (in the
       SHFT(dum,*fb,*fa,dum)    case of a health survey which is our main interest) -2- at least a
       }    second wave of interviews ("longitudinal") which measure each change
   *cx=(*bx)+GOLD*(*bx-*ax);    (if any) in individual health status.  Health expectancies are
   *fc=(*func)(*cx);    computed from the time spent in each health state according to a
   while (*fb > *fc) {    model. More health states you consider, more time is necessary to reach the
     r=(*bx-*ax)*(*fb-*fc);    Maximum Likelihood of the parameters involved in the model.  The
     q=(*bx-*cx)*(*fb-*fa);    simplest model is the multinomial logistic model where pij is the
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    probability to be observed in state j at the second wave
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    conditional to be observed in state i at the first wave. Therefore
     ulim=(*bx)+GLIMIT*(*cx-*bx);    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     if ((*bx-u)*(u-*cx) > 0.0) {    'age' is age and 'sex' is a covariate. If you want to have a more
       fu=(*func)(u);    complex model than "constant and age", you should modify the program
     } else if ((*cx-u)*(u-ulim) > 0.0) {    where the markup *Covariates have to be included here again* invites
       fu=(*func)(u);    you to do it.  More covariates you add, slower the
       if (fu < *fc) {    convergence.
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))    The advantage of this computer programme, compared to a simple
           }    multinomial logistic model, is clear when the delay between waves is not
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    identical for each individual. Also, if a individual missed an
       u=ulim;    intermediate interview, the information is lost, but taken into
       fu=(*func)(u);    account using an interpolation or extrapolation.  
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);    hPijx is the probability to be observed in state i at age x+h
       fu=(*func)(u);    conditional to the observed state i at age x. The delay 'h' can be
     }    split into an exact number (nh*stepm) of unobserved intermediate
     SHFT(*ax,*bx,*cx,u)    states. This elementary transition (by month, quarter,
       SHFT(*fa,*fb,*fc,fu)    semester or year) is modelled as a multinomial logistic.  The hPx
       }    matrix is simply the matrix product of nh*stepm elementary matrices
 }    and the contribution of each individual to the likelihood is simply
     hPijx.
 /*************** linmin ************************/  
     Also this programme outputs the covariance matrix of the parameters but also
 int ncom;    of the life expectancies. It also computes the period (stable) prevalence. 
 double *pcom,*xicom;    
 double (*nrfunc)(double []);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
               Institut national d'études démographiques, Paris.
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    This software have been partly granted by Euro-REVES, a concerted action
 {    from the European Union.
   double brent(double ax, double bx, double cx,    It is copyrighted identically to a GNU software product, ie programme and
                double (*f)(double), double tol, double *xmin);    software can be distributed freely for non commercial use. Latest version
   double f1dim(double x);    can be accessed at http://euroreves.ined.fr/imach .
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   int j;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   double xx,xmin,bx,ax;    
   double fx,fb,fa;    **********************************************************************/
    /*
   ncom=n;    main
   pcom=vector(1,n);    read parameterfile
   xicom=vector(1,n);    read datafile
   nrfunc=func;    concatwav
   for (j=1;j<=n;j++) {    freqsummary
     pcom[j]=p[j];    if (mle >= 1)
     xicom[j]=xi[j];      mlikeli
   }    print results files
   ax=0.0;    if mle==1 
   xx=1.0;       computes hessian
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    read end of parameter file: agemin, agemax, bage, fage, estepm
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);        begin-prev-date,...
 #ifdef DEBUG    open gnuplot file
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    open html file
 #endif    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
   for (j=1;j<=n;j++) {     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
     xi[j] *= xmin;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
     p[j] += xi[j];      freexexit2 possible for memory heap.
   }  
   free_vector(xicom,1,n);    h Pij x                         | pij_nom  ficrestpij
   free_vector(pcom,1,n);     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
 }         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
          1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
             double (*func)(double []))         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
 {    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   void linmin(double p[], double xi[], int n, double *fret,     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
               double (*func)(double []));     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;    forecasting if prevfcast==1 prevforecast call prevalence()
   double fp,fptt;    health expectancies
   double *xits;    Variance-covariance of DFLE
   pt=vector(1,n);    prevalence()
   ptt=vector(1,n);     movingaverage()
   xit=vector(1,n);    varevsij() 
   xits=vector(1,n);    if popbased==1 varevsij(,popbased)
   *fret=(*func)(p);    total life expectancies
   for (j=1;j<=n;j++) pt[j]=p[j];    Variance of period (stable) prevalence
   for (*iter=1;;++(*iter)) {   end
     fp=(*fret);  */
     ibig=0;  
     del=0.0;  #define POWELL /* Instead of NLOPT */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /* #define POWELLORIGINAL */ /* Don't use Directest to decide new direction but original Powell test */
     for (i=1;i<=n;i++)  /* #define MNBRAKORIGINAL */ /* Don't use mnbrak fix */
       printf(" %d %.12f",i, p[i]);  
     printf("\n");  #include <math.h>
     for (i=1;i<=n;i++) {  #include <stdio.h>
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  #include <stdlib.h>
       fptt=(*fret);  #include <string.h>
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  #ifdef _WIN32
 #endif  #include <io.h>
       printf("%d",i);fflush(stdout);  #include <windows.h>
       linmin(p,xit,n,fret,func);  #include <tchar.h>
       if (fabs(fptt-(*fret)) > del) {  #else
         del=fabs(fptt-(*fret));  #include <unistd.h>
         ibig=i;  #endif
       }  
 #ifdef DEBUG  #include <limits.h>
       printf("%d %.12e",i,(*fret));  #include <sys/types.h>
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #if defined(__GNUC__)
         printf(" x(%d)=%.12e",j,xit[j]);  #include <sys/utsname.h> /* Doesn't work on Windows */
       }  #endif
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);  #include <sys/stat.h>
       printf("\n");  #include <errno.h>
 #endif  /* extern int errno; */
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  /* #ifdef LINUX */
 #ifdef DEBUG  /* #include <time.h> */
       int k[2],l;  /* #include "timeval.h" */
       k[0]=1;  /* #else */
       k[1]=-1;  /* #include <sys/time.h> */
       printf("Max: %.12e",(*func)(p));  /* #endif */
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  #include <time.h>
       printf("\n");  
       for(l=0;l<=1;l++) {  #ifdef GSL
         for (j=1;j<=n;j++) {  #include <gsl/gsl_errno.h>
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  #include <gsl/gsl_multimin.h>
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  #endif
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  #ifdef NLOPT
 #endif  #include <nlopt.h>
   typedef struct {
     double (* function)(double [] );
       free_vector(xit,1,n);  } myfunc_data ;
       free_vector(xits,1,n);  #endif
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);  /* #include <libintl.h> */
       return;  /* #define _(String) gettext (String) */
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];  #define GNUPLOTPROGRAM "gnuplot"
       xit[j]=p[j]-pt[j];  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       pt[j]=p[j];  #define FILENAMELENGTH 132
     }  
     fptt=(*func)(ptt);  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
     if (fptt < fp) {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
         linmin(p,xit,n,fret,func);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];  #define NINTERVMAX 8
           xi[j][n]=xit[j];  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
         }  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 #ifdef DEBUG  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
         for(j=1;j<=n;j++)  #define MAXN 20000
           printf(" %.12e",xit[j]);  #define YEARM 12. /**< Number of months per year */
         printf("\n");  #define AGESUP 130
 #endif  #define AGEBASE 40
       }  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
     }  #ifdef _WIN32
   }  #define DIRSEPARATOR '\\'
 }  #define CHARSEPARATOR "\\"
   #define ODIRSEPARATOR '/'
 /**** Prevalence limit ****************/  #else
   #define DIRSEPARATOR '/'
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  #define CHARSEPARATOR "/"
 {  #define ODIRSEPARATOR '\\'
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  #endif
      matrix by transitions matrix until convergence is reached */  
   /* $Id$ */
   int i, ii,j,k;  /* $State$ */
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();  char version[]="Imach version 0.98q0, March 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
   double **out, cov[NCOVMAX], **pmij();  char fullversion[]="$Revision$ $Date$"; 
   double **newm;  char strstart[80];
   double agefin, delaymax=50 ; /* Max number of years to converge */  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   for (ii=1;ii<=nlstate+ndeath;ii++)  int nvar=0, nforce=0; /* Number of variables, number of forces */
     for (j=1;j<=nlstate+ndeath;j++){  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
     }  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
    cov[1]=1.;  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
    int cptcovprodnoage=0; /**< Number of covariate products without age */   
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  int cptcov=0; /* Working variable */
     newm=savm;  int npar=NPARMAX;
     /* Covariates have to be included here again */  int nlstate=2; /* Number of live states */
      cov[2]=agefin;  int ndeath=1; /* Number of dead states */
    int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       for (k=1; k<=cptcovn;k++) {  int popbased=0;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  int *wav; /* Number of waves for this individuual 0 is possible */
       }  int maxwav=0; /* Maxim number of waves */
       for (k=1; k<=cptcovage;k++)  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       for (k=1; k<=cptcovprod;k++)  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];                     to the likelihood and the sum of weights (done by funcone)*/
   int mle=1, weightopt=0;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  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
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   int countcallfunc=0;  /* Count the number of calls to func */
     savm=oldm;  double jmean=1; /* Mean space between 2 waves */
     oldm=newm;  double **matprod2(); /* test */
     maxmax=0.;  double **oldm, **newm, **savm; /* Working pointers to matrices */
     for(j=1;j<=nlstate;j++){  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       min=1.;  /*FILE *fic ; */ /* Used in readdata only */
       max=0.;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       for(i=1; i<=nlstate; i++) {  FILE *ficlog, *ficrespow;
         sumnew=0;  int globpr=0; /* Global variable for printing or not */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  double fretone; /* Only one call to likelihood */
         prlim[i][j]= newm[i][j]/(1-sumnew);  long ipmx=0; /* Number of contributions */
         max=FMAX(max,prlim[i][j]);  double sw; /* Sum of weights */
         min=FMIN(min,prlim[i][j]);  char filerespow[FILENAMELENGTH];
       }  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       maxmin=max-min;  FILE *ficresilk;
       maxmax=FMAX(maxmax,maxmin);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     }  FILE *ficresprobmorprev;
     if(maxmax < ftolpl){  FILE *fichtm, *fichtmcov; /* Html File */
       return prlim;  FILE *ficreseij;
     }  char filerese[FILENAMELENGTH];
   }  FILE *ficresstdeij;
 }  char fileresstde[FILENAMELENGTH];
   FILE *ficrescveij;
 /*************** transition probabilities ***************/  char filerescve[FILENAMELENGTH];
   FILE  *ficresvij;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  char fileresv[FILENAMELENGTH];
 {  FILE  *ficresvpl;
   double s1, s2;  char fileresvpl[FILENAMELENGTH];
   /*double t34;*/  char title[MAXLINE];
   int i,j,j1, nc, ii, jj;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     for(i=1; i<= nlstate; i++){  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     for(j=1; j<i;j++){  char command[FILENAMELENGTH];
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  int  outcmd=0;
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  char filelog[FILENAMELENGTH]; /* Log file */
       ps[i][j]=s2;  char filerest[FILENAMELENGTH];
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  char fileregp[FILENAMELENGTH];
     }  char popfile[FILENAMELENGTH];
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
       }  /* struct timezone tzp; */
       ps[i][j]=s2;  /* extern int gettimeofday(); */
     }  struct tm tml, *gmtime(), *localtime();
   }  
     /*ps[3][2]=1;*/  extern time_t time();
   
   for(i=1; i<= nlstate; i++){  struct tm start_time, end_time, curr_time, last_time, forecast_time;
      s1=0;  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
     for(j=1; j<i; j++)  struct tm tm;
       s1+=exp(ps[i][j]);  
     for(j=i+1; j<=nlstate+ndeath; j++)  char strcurr[80], strfor[80];
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);  char *endptr;
     for(j=1; j<i; j++)  long lval;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  double dval;
     for(j=i+1; j<=nlstate+ndeath; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #define NR_END 1
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  #define FREE_ARG char*
   } /* end i */  #define FTOL 1.0e-10
   
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  #define NRANSI 
     for(jj=1; jj<= nlstate+ndeath; jj++){  #define ITMAX 200 
       ps[ii][jj]=0;  
       ps[ii][ii]=1;  #define TOL 2.0e-4 
     }  
   }  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  #define GOLD 1.618034 
      printf("%lf ",ps[ii][jj]);  #define GLIMIT 100.0 
    }  #define TINY 1.0e-20 
     printf("\n ");  
     }  static double maxarg1,maxarg2;
     printf("\n ");printf("%lf ",cov[2]);*/  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 /*  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    
   goto end;*/  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     return ps;  #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
 /**************** Product of 2 matrices ******************/  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
   /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  /* static double dsqrarg; */
 {  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  static double sqrarg;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   /* in, b, out are matrice of pointers which should have been initialized  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
      before: only the contents of out is modified. The function returns  int agegomp= AGEGOMP;
      a pointer to pointers identical to out */  
   long i, j, k;  int imx; 
   for(i=nrl; i<= nrh; i++)  int stepm=1;
     for(k=ncolol; k<=ncoloh; k++)  /* Stepm, step in month: minimum step interpolation*/
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];  int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   return out;  
 }  int m,nb;
   long *num;
   int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 /************* Higher Matrix Product ***************/  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  double *ageexmed,*agecens;
 {  double dateintmean=0;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  
      duration (i.e. until  double *weight;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  int **s; /* Status */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  double *agedc;
      (typically every 2 years instead of every month which is too big).  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
      Model is determined by parameters x and covariates have to be                    * covar=matrix(0,NCOVMAX,1,n); 
      included manually here.                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
   double  idx; 
      */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   int *Ndum; /** Freq of modality (tricode */
   int i, j, d, h, k;  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   double **out, cov[NCOVMAX];  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double **newm;  double *lsurv, *lpop, *tpop;
   
   /* Hstepm could be zero and should return the unit matrix */  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   for (i=1;i<=nlstate+ndeath;i++)  double ftolhess; /**< Tolerance for computing hessian */
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);  /**************** split *************************/
       po[i][j][0]=(i==j ? 1.0 : 0.0);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     }  {
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   for(h=1; h <=nhstepm; h++){       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     for(d=1; d <=hstepm; d++){    */ 
       newm=savm;    char  *ss;                            /* pointer */
       /* Covariates have to be included here again */    int   l1, l2;                         /* length counters */
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    l1 = strlen(path );                   /* length of path */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       for (k=1; k<=cptcovage;k++)    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       for (k=1; k<=cptcovprod;k++)      strcpy( name, path );               /* we got the fullname name because no directory */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       /* get current working directory */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      /*    extern  char* getcwd ( char *buf , int len);*/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  #ifdef WIN32
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  #else
       savm=oldm;          if (getcwd(dirc, FILENAME_MAX) == NULL) {
       oldm=newm;  #endif
     }        return( GLOCK_ERROR_GETCWD );
     for(i=1; i<=nlstate+ndeath; i++)      }
       for(j=1;j<=nlstate+ndeath;j++) {      /* got dirc from getcwd*/
         po[i][j][h]=newm[i][j];      printf(" DIRC = %s \n",dirc);
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    } else {                              /* strip direcotry from path */
          */      ss++;                               /* after this, the filename */
       }      l2 = strlen( ss );                  /* length of filename */
   } /* end h */      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   return po;      strcpy( name, ss );         /* save file name */
 }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
       printf(" DIRC2 = %s \n",dirc);
 /*************** log-likelihood *************/    }
 double func( double *x)    /* We add a separator at the end of dirc if not exists */
 {    l1 = strlen( dirc );                  /* length of directory */
   int i, ii, j, k, mi, d, kk;    if( dirc[l1-1] != DIRSEPARATOR ){
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      dirc[l1] =  DIRSEPARATOR;
   double **out;      dirc[l1+1] = 0; 
   double sw; /* Sum of weights */      printf(" DIRC3 = %s \n",dirc);
   double lli; /* Individual log likelihood */    }
   long ipmx;    ss = strrchr( name, '.' );            /* find last / */
   /*extern weight */    if (ss >0){
   /* We are differentiating ll according to initial status */      ss++;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      strcpy(ext,ss);                     /* save extension */
   /*for(i=1;i<imx;i++)      l1= strlen( name);
     printf(" %d\n",s[4][i]);      l2= strlen(ss)+1;
   */      strncpy( finame, name, l1-l2);
   cov[1]=1.;      finame[l1-l2]= 0;
     }
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    return( 0 );                          /* we're done */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  }
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)  
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /******************************************/
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;  void replace_back_to_slash(char *s, char*t)
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  {
         for (kk=1; kk<=cptcovage;kk++) {    int i;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    int lg=0;
         }    i=0;
            lg=strlen(t);
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    for(i=0; i<= lg; i++) {
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      (s[i] = t[i]);
         savm=oldm;      if (t[i]== '\\') s[i]='/';
         oldm=newm;    }
          }
          
       } /* end mult */  char *trimbb(char *out, char *in)
        { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    char *s;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    s=out;
       ipmx +=1;    while (*in != '\0'){
       sw += weight[i];      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        in++;
     } /* end of wave */      }
   } /* end of individual */      *out++ = *in++;
     }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    *out='\0';
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    return s;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  }
   return -l;  
 }  char *cutl(char *blocc, char *alocc, char *in, char occ)
   {
     /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
 /*********** Maximum Likelihood Estimation ***************/       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef2ghi" and alocc="j".
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))       If occ is not found blocc is null and alocc is equal to in. Returns blocc
 {    */
   int i,j, iter;    char *s, *t;
   double **xi,*delti;    t=in;s=in;
   double fret;    while ((*in != occ) && (*in != '\0')){
   xi=matrix(1,npar,1,npar);      *alocc++ = *in++;
   for (i=1;i<=npar;i++)    }
     for (j=1;j<=npar;j++)    if( *in == occ){
       xi[i][j]=(i==j ? 1.0 : 0.0);      *(alocc)='\0';
   printf("Powell\n");      s=++in;
   powell(p,xi,npar,ftol,&iter,&fret,func);    }
    
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    if (s == t) {/* occ not found */
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      *(alocc-(in-s))='\0';
       in=s;
 }    }
     while ( *in != '\0'){
 /**** Computes Hessian and covariance matrix ***/      *blocc++ = *in++;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    }
 {  
   double  **a,**y,*x,pd;    *blocc='\0';
   double **hess;    return t;
   int i, j,jk;  }
   int *indx;  char *cutv(char *blocc, char *alocc, char *in, char occ)
   {
   double hessii(double p[], double delta, int theta, double delti[]);    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
   double hessij(double p[], double delti[], int i, int j);       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   void lubksb(double **a, int npar, int *indx, double b[]) ;       gives blocc="abcdef2ghi" and alocc="j".
   void ludcmp(double **a, int npar, int *indx, double *d) ;       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     */
   hess=matrix(1,npar,1,npar);    char *s, *t;
     t=in;s=in;
   printf("\nCalculation of the hessian matrix. Wait...\n");    while (*in != '\0'){
   for (i=1;i<=npar;i++){      while( *in == occ){
     printf("%d",i);fflush(stdout);        *blocc++ = *in++;
     hess[i][i]=hessii(p,ftolhess,i,delti);        s=in;
     /*printf(" %f ",p[i]);*/      }
     /*printf(" %lf ",hess[i][i]);*/      *blocc++ = *in++;
   }    }
      if (s == t) /* occ not found */
   for (i=1;i<=npar;i++) {      *(blocc-(in-s))='\0';
     for (j=1;j<=npar;j++)  {    else
       if (j>i) {      *(blocc-(in-s)-1)='\0';
         printf(".%d%d",i,j);fflush(stdout);    in=s;
         hess[i][j]=hessij(p,delti,i,j);    while ( *in != '\0'){
         hess[j][i]=hess[i][j];          *alocc++ = *in++;
         /*printf(" %lf ",hess[i][j]);*/    }
       }  
     }    *alocc='\0';
   }    return s;
   printf("\n");  }
   
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  int nbocc(char *s, char occ)
    {
   a=matrix(1,npar,1,npar);    int i,j=0;
   y=matrix(1,npar,1,npar);    int lg=20;
   x=vector(1,npar);    i=0;
   indx=ivector(1,npar);    lg=strlen(s);
   for (i=1;i<=npar;i++)    for(i=0; i<= lg; i++) {
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    if  (s[i] == occ ) j++;
   ludcmp(a,npar,indx,&pd);    }
     return j;
   for (j=1;j<=npar;j++) {  }
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  /* void cutv(char *u,char *v, char*t, char occ) */
     lubksb(a,npar,indx,x);  /* { */
     for (i=1;i<=npar;i++){  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
       matcov[i][j]=x[i];  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     }  /*      gives u="abcdef2ghi" and v="j" *\/ */
   }  /*   int i,lg,j,p=0; */
   /*   i=0; */
   printf("\n#Hessian matrix#\n");  /*   lg=strlen(t); */
   for (i=1;i<=npar;i++) {  /*   for(j=0; j<=lg-1; j++) { */
     for (j=1;j<=npar;j++) {  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
       printf("%.3e ",hess[i][j]);  /*   } */
     }  
     printf("\n");  /*   for(j=0; j<p; j++) { */
   }  /*     (u[j] = t[j]); */
   /*   } */
   /* Recompute Inverse */  /*      u[p]='\0'; */
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  /*    for(j=0; j<= lg; j++) { */
   ludcmp(a,npar,indx,&pd);  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /*   } */
   /*  printf("\n#Hessian matrix recomputed#\n");  /* } */
   
   for (j=1;j<=npar;j++) {  #ifdef _WIN32
     for (i=1;i<=npar;i++) x[i]=0;  char * strsep(char **pp, const char *delim)
     x[j]=1;  {
     lubksb(a,npar,indx,x);    char *p, *q;
     for (i=1;i<=npar;i++){           
       y[i][j]=x[i];    if ((p = *pp) == NULL)
       printf("%.3e ",y[i][j]);      return 0;
     }    if ((q = strpbrk (p, delim)) != NULL)
     printf("\n");    {
   }      *pp = q + 1;
   */      *q = '\0';
     }
   free_matrix(a,1,npar,1,npar);    else
   free_matrix(y,1,npar,1,npar);      *pp = 0;
   free_vector(x,1,npar);    return p;
   free_ivector(indx,1,npar);  }
   free_matrix(hess,1,npar,1,npar);  #endif
   
   /********************** nrerror ********************/
 }  
   void nrerror(char error_text[])
 /*************** hessian matrix ****************/  {
 double hessii( double x[], double delta, int theta, double delti[])    fprintf(stderr,"ERREUR ...\n");
 {    fprintf(stderr,"%s\n",error_text);
   int i;    exit(EXIT_FAILURE);
   int l=1, lmax=20;  }
   double k1,k2;  /*********************** vector *******************/
   double p2[NPARMAX+1];  double *vector(int nl, int nh)
   double res;  {
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double *v;
   double fx;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   int k=0,kmax=10;    if (!v) nrerror("allocation failure in vector");
   double l1;    return v-nl+NR_END;
   }
   fx=func(x);  
   for (i=1;i<=npar;i++) p2[i]=x[i];  /************************ free vector ******************/
   for(l=0 ; l <=lmax; l++){  void free_vector(double*v, int nl, int nh)
     l1=pow(10,l);  {
     delts=delt;    free((FREE_ARG)(v+nl-NR_END));
     for(k=1 ; k <kmax; k=k+1){  }
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;  /************************ivector *******************************/
       k1=func(p2)-fx;  int *ivector(long nl,long nh)
       p2[theta]=x[theta]-delt;  {
       k2=func(p2)-fx;    int *v;
       /*res= (k1-2.0*fx+k2)/delt/delt; */    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    if (!v) nrerror("allocation failure in ivector");
          return v-nl+NR_END;
 #ifdef DEBUG  }
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  
 #endif  /******************free ivector **************************/
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  void free_ivector(int *v, long nl, long nh)
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  {
         k=kmax;    free((FREE_ARG)(v+nl-NR_END));
       }  }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  
         k=kmax; l=lmax*10.;  /************************lvector *******************************/
       }  long *lvector(long nl,long nh)
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  {
         delts=delt;    long *v;
       }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     }    if (!v) nrerror("allocation failure in ivector");
   }    return v-nl+NR_END;
   delti[theta]=delts;  }
   return res;  
    /******************free lvector **************************/
 }  void free_lvector(long *v, long nl, long nh)
   {
 double hessij( double x[], double delti[], int thetai,int thetaj)    free((FREE_ARG)(v+nl-NR_END));
 {  }
   int i;  
   int l=1, l1, lmax=20;  /******************* imatrix *******************************/
   double k1,k2,k3,k4,res,fx;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   double p2[NPARMAX+1];       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   int k;  { 
     long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   fx=func(x);    int **m; 
   for (k=1; k<=2; k++) {    
     for (i=1;i<=npar;i++) p2[i]=x[i];    /* allocate pointers to rows */ 
     p2[thetai]=x[thetai]+delti[thetai]/k;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    if (!m) nrerror("allocation failure 1 in matrix()"); 
     k1=func(p2)-fx;    m += NR_END; 
      m -= nrl; 
     p2[thetai]=x[thetai]+delti[thetai]/k;    
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    
     k2=func(p2)-fx;    /* allocate rows and set pointers to them */ 
      m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     p2[thetai]=x[thetai]-delti[thetai]/k;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    m[nrl] += NR_END; 
     k3=func(p2)-fx;    m[nrl] -= ncl; 
      
     p2[thetai]=x[thetai]-delti[thetai]/k;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    
     k4=func(p2)-fx;    /* return pointer to array of pointers to rows */ 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    return m; 
 #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  /****************** free_imatrix *************************/
   }  void free_imatrix(m,nrl,nrh,ncl,nch)
   return res;        int **m;
 }        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
 /************** Inverse of matrix **************/  { 
 void ludcmp(double **a, int n, int *indx, double *d)    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 {    free((FREE_ARG) (m+nrl-NR_END)); 
   int i,imax,j,k;  } 
   double big,dum,sum,temp;  
   double *vv;  /******************* matrix *******************************/
    double **matrix(long nrl, long nrh, long ncl, long nch)
   vv=vector(1,n);  {
   *d=1.0;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   for (i=1;i<=n;i++) {    double **m;
     big=0.0;  
     for (j=1;j<=n;j++)    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       if ((temp=fabs(a[i][j])) > big) big=temp;    if (!m) nrerror("allocation failure 1 in matrix()");
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    m += NR_END;
     vv[i]=1.0/big;    m -= nrl;
   }  
   for (j=1;j<=n;j++) {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     for (i=1;i<j;i++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       sum=a[i][j];    m[nrl] += NR_END;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    m[nrl] -= ncl;
       a[i][j]=sum;  
     }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     big=0.0;    return m;
     for (i=j;i<=n;i++) {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
       sum=a[i][j];  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
       for (k=1;k<j;k++)  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
         sum -= a[i][k]*a[k][j];     */
       a[i][j]=sum;  }
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;  /*************************free matrix ************************/
         imax=i;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       }  {
     }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     if (j != imax) {    free((FREE_ARG)(m+nrl-NR_END));
       for (k=1;k<=n;k++) {  }
         dum=a[imax][k];  
         a[imax][k]=a[j][k];  /******************* ma3x *******************************/
         a[j][k]=dum;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       }  {
       *d = -(*d);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       vv[imax]=vv[j];    double ***m;
     }  
     indx[j]=imax;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (a[j][j] == 0.0) a[j][j]=TINY;    if (!m) nrerror("allocation failure 1 in matrix()");
     if (j != n) {    m += NR_END;
       dum=1.0/(a[j][j]);    m -= nrl;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free_vector(vv,1,n);  /* Doesn't work */    m[nrl] += NR_END;
 ;    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 void lubksb(double **a, int n, int *indx, double b[])  
 {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   int i,ii=0,ip,j;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   double sum;    m[nrl][ncl] += NR_END;
      m[nrl][ncl] -= nll;
   for (i=1;i<=n;i++) {    for (j=ncl+1; j<=nch; j++) 
     ip=indx[i];      m[nrl][j]=m[nrl][j-1]+nlay;
     sum=b[ip];    
     b[ip]=b[i];    for (i=nrl+1; i<=nrh; i++) {
     if (ii)      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      for (j=ncl+1; j<=nch; j++) 
     else if (sum) ii=i;        m[i][j]=m[i][j-1]+nlay;
     b[i]=sum;    }
   }    return m; 
   for (i=n;i>=1;i--) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     sum=b[i];             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    */
     b[i]=sum/a[i][i];  }
   }  
 }  /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 /************ Frequencies ********************/  {
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 {  /* Some frequencies */    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      free((FREE_ARG)(m+nrl-NR_END));
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  }
   double ***freq; /* Frequencies */  
   double *pp;  /*************** function subdirf ***********/
   double pos, k2, dateintsum=0,k2cpt=0;  char *subdirf(char fileres[])
   FILE *ficresp;  {
   char fileresp[FILENAMELENGTH];    /* Caution optionfilefiname is hidden */
      strcpy(tmpout,optionfilefiname);
   pp=vector(1,nlstate);    strcat(tmpout,"/"); /* Add to the right */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    strcat(tmpout,fileres);
   strcpy(fileresp,"p");    return tmpout;
   strcat(fileresp,fileres);  }
   if((ficresp=fopen(fileresp,"w"))==NULL) {  
     printf("Problem with prevalence resultfile: %s\n", fileresp);  /*************** function subdirf2 ***********/
     exit(0);  char *subdirf2(char fileres[], char *preop)
   }  {
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    
   j1=0;    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   j=cptcoveff;    strcat(tmpout,"/");
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    strcat(tmpout,preop);
     strcat(tmpout,fileres);
   for(k1=1; k1<=j;k1++){    return tmpout;
    for(i1=1; i1<=ncodemax[k1];i1++){  }
        j1++;  
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  /*************** function subdirf3 ***********/
          scanf("%d", i);*/  char *subdirf3(char fileres[], char *preop, char *preop2)
         for (i=-1; i<=nlstate+ndeath; i++)    {
          for (jk=-1; jk<=nlstate+ndeath; jk++)      
            for(m=agemin; m <= agemax+3; m++)    /* Caution optionfilefiname is hidden */
              freq[i][jk][m]=0;    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
         dateintsum=0;    strcat(tmpout,preop);
         k2cpt=0;    strcat(tmpout,preop2);
        for (i=1; i<=imx; i++) {    strcat(tmpout,fileres);
          bool=1;    return tmpout;
          if  (cptcovn>0) {  }
            for (z1=1; z1<=cptcoveff; z1++)  
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  char *asc_diff_time(long time_sec, char ascdiff[])
                bool=0;  {
          }    long sec_left, days, hours, minutes;
          if (bool==1) {    days = (time_sec) / (60*60*24);
            for(m=firstpass; m<=lastpass; m++){    sec_left = (time_sec) % (60*60*24);
              k2=anint[m][i]+(mint[m][i]/12.);    hours = (sec_left) / (60*60) ;
              if ((k2>=dateprev1) && (k2<=dateprev2)) {    sec_left = (sec_left) %(60*60);
                if(agev[m][i]==0) agev[m][i]=agemax+1;    minutes = (sec_left) /60;
                if(agev[m][i]==1) agev[m][i]=agemax+2;    sec_left = (sec_left) % (60);
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    return ascdiff;
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  }
                  dateintsum=dateintsum+k2;  
                  k2cpt++;  /***************** f1dim *************************/
                }  extern int ncom; 
   extern double *pcom,*xicom;
              }  extern double (*nrfunc)(double []); 
            }   
          }  double f1dim(double x) 
        }  { 
            int j; 
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    double f;
     double *xt; 
         if  (cptcovn>0) {   
          fprintf(ficresp, "\n#********** Variable ");    xt=vector(1,ncom); 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
        fprintf(ficresp, "**********\n#");    f=(*nrfunc)(xt); 
         }    free_vector(xt,1,ncom); 
        for(i=1; i<=nlstate;i++)    return f; 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  } 
        fprintf(ficresp, "\n");  
          /*****************brent *************************/
   for(i=(int)agemin; i <= (int)agemax+3; i++){  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     if(i==(int)agemax+3)  { 
       printf("Total");    int iter; 
     else    double a,b,d,etemp;
       printf("Age %d", i);    double fu=0,fv,fw,fx;
     for(jk=1; jk <=nlstate ; jk++){    double ftemp=0.;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         pp[jk] += freq[jk][m][i];    double e=0.0; 
     }   
     for(jk=1; jk <=nlstate ; jk++){    a=(ax < cx ? ax : cx); 
       for(m=-1, pos=0; m <=0 ; m++)    b=(ax > cx ? ax : cx); 
         pos += freq[jk][m][i];    x=w=v=bx; 
       if(pp[jk]>=1.e-10)    fw=fv=fx=(*f)(x); 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    for (iter=1;iter<=ITMAX;iter++) { 
       else      xm=0.5*(a+b); 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
      for(jk=1; jk <=nlstate ; jk++){      fprintf(ficlog,".");fflush(ficlog);
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  #ifdef DEBUGBRENT
         pp[jk] += freq[jk][m][i];      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
      }      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     for(jk=1,pos=0; jk <=nlstate ; jk++)  #endif
       pos += pp[jk];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     for(jk=1; jk <=nlstate ; jk++){        *xmin=x; 
       if(pos>=1.e-5)        return fx; 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      } 
       else      ftemp=fu;
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      if (fabs(e) > tol1) { 
       if( i <= (int) agemax){        r=(x-w)*(fx-fv); 
         if(pos>=1.e-5){        q=(x-v)*(fx-fw); 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        p=(x-v)*q-(x-w)*r; 
           probs[i][jk][j1]= pp[jk]/pos;        q=2.0*(q-r); 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        if (q > 0.0) p = -p; 
         }        q=fabs(q); 
       else        etemp=e; 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        e=d; 
       }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for(jk=-1; jk <=nlstate+ndeath; jk++)        else { 
       for(m=-1; m <=nlstate+ndeath; m++)          d=p/q; 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          u=x+d; 
     if(i <= (int) agemax)          if (u-a < tol2 || b-u < tol2) 
       fprintf(ficresp,"\n");            d=SIGN(tol1,xm-x); 
     printf("\n");        } 
     }      } else { 
     }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
  }      } 
   dateintmean=dateintsum/k2cpt;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
        fu=(*f)(u); 
   fclose(ficresp);      if (fu <= fx) { 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        if (u >= x) a=x; else b=x; 
   free_vector(pp,1,nlstate);        SHFT(v,w,x,u) 
         SHFT(fv,fw,fx,fu) 
   /* End of Freq */      } else { 
 }        if (u < x) a=u; else b=u; 
         if (fu <= fw || w == x) { 
 /************ Prevalence ********************/          v=w; 
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)          w=u; 
 {  /* Some frequencies */          fv=fw; 
            fw=fu; 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        } else if (fu <= fv || v == x || v == w) { 
   double ***freq; /* Frequencies */          v=u; 
   double *pp;          fv=fu; 
   double pos, k2;        } 
       } 
   pp=vector(1,nlstate);    } 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    nrerror("Too many iterations in brent"); 
      *xmin=x; 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    return fx; 
   j1=0;  } 
    
   j=cptcoveff;  /****************** mnbrak ***********************/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
  for(k1=1; k1<=j;k1++){              double (*func)(double)) 
     for(i1=1; i1<=ncodemax[k1];i1++){  { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
       j1++;  the downhill direction (defined by the function as evaluated at the initial points) and returns
    new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
       for (i=-1; i<=nlstate+ndeath; i++)    values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
         for (jk=-1; jk<=nlstate+ndeath; jk++)       */
           for(m=agemin; m <= agemax+3; m++)    double ulim,u,r,q, dum;
             freq[i][jk][m]=0;    double fu; 
         
       for (i=1; i<=imx; i++) {    *fa=(*func)(*ax); 
         bool=1;    *fb=(*func)(*bx); 
         if  (cptcovn>0) {    if (*fb > *fa) { 
           for (z1=1; z1<=cptcoveff; z1++)      SHFT(dum,*ax,*bx,dum) 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      SHFT(dum,*fb,*fa,dum) 
               bool=0;    } 
         }    *cx=(*bx)+GOLD*(*bx-*ax); 
         if (bool==1) {    *fc=(*func)(*cx); 
           for(m=firstpass; m<=lastpass; m++){  #ifdef DEBUG
             k2=anint[m][i]+(mint[m][i]/12.);    printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
               if(agev[m][i]==0) agev[m][i]=agemax+1;  #endif
               if(agev[m][i]==1) agev[m][i]=agemax+2;    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      r=(*bx-*ax)*(*fb-*fc); 
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */      q=(*bx-*cx)*(*fb-*fa); 
             }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
           }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
         }      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
       }      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
         for(i=(int)agemin; i <= (int)agemax+3; i++){        fu=(*func)(u); 
           for(jk=1; jk <=nlstate ; jk++){  #ifdef DEBUG
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        /* f(x)=A(x-u)**2+f(u) */
               pp[jk] += freq[jk][m][i];        double A, fparabu; 
           }        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
           for(jk=1; jk <=nlstate ; jk++){        fparabu= *fa - A*(*ax-u)*(*ax-u);
             for(m=-1, pos=0; m <=0 ; m++)        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);
             pos += freq[jk][m][i];        fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
         }        /* And thus,it can be that fu > *fc even if fparabu < *fc */
                /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
          for(jk=1; jk <=nlstate ; jk++){          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
              pp[jk] += freq[jk][m][i];  #endif 
          }  #ifdef MNBRAKORIGINAL
            #else
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        if (fu > *fc) {
   #ifdef DEBUG
          for(jk=1; jk <=nlstate ; jk++){                  printf("mnbrak4  fu > fc \n");
            if( i <= (int) agemax){        fprintf(ficlog, "mnbrak4 fu > fc\n");
              if(pos>=1.e-5){  #endif
                probs[i][jk][j1]= pp[jk]/pos;          /* SHFT(u,*cx,*cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\/  */
              }          /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\/ */
            }          dum=u; /* Shifting c and u */
          }          u = *cx;
                    *cx = dum;
         }          dum = fu;
     }          fu = *fc;
   }          *fc =dum;
          } else { /* end */
    #ifdef DEBUG
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        printf("mnbrak3  fu < fc \n");
   free_vector(pp,1,nlstate);        fprintf(ficlog, "mnbrak3 fu < fc\n");
    #endif
 }  /* End of Freq */          dum=u; /* Shifting c and u */
           u = *cx;
 /************* Waves Concatenation ***************/          *cx = dum;
           dum = fu;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          fu = *fc;
 {          *fc =dum;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        }
      Death is a valid wave (if date is known).  #endif
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  #ifdef DEBUG
      and mw[mi+1][i]. dh depends on stepm.        printf("mnbrak2  u after c but before ulim\n");
      */        fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
   #endif
   int i, mi, m;        fu=(*func)(u); 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        if (fu < *fc) { 
      double sum=0., jmean=0.;*/  #ifdef DEBUG
         printf("mnbrak2  u after c but before ulim AND fu < fc\n");
   int j, k=0,jk, ju, jl;        fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
   double sum=0.;  #endif
   jmin=1e+5;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   jmax=-1;          SHFT(*fb,*fc,fu,(*func)(u)) 
   jmean=0.;        } 
   for(i=1; i<=imx; i++){      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
     mi=0;  #ifdef DEBUG
     m=firstpass;        printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
     while(s[m][i] <= nlstate){        fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
       if(s[m][i]>=1)  #endif
         mw[++mi][i]=m;        u=ulim; 
       if(m >=lastpass)        fu=(*func)(u); 
         break;      } else { /* u could be left to b (if r > q parabola has a maximum) */
       else  #ifdef DEBUG
         m++;        printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
     }/* end while */        fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
     if (s[m][i] > nlstate){  #endif
       mi++;     /* Death is another wave */        u=(*cx)+GOLD*(*cx-*bx); 
       /* if(mi==0)  never been interviewed correctly before death */        fu=(*func)(u); 
          /* Only death is a correct wave */      } /* end tests */
       mw[mi][i]=m;      SHFT(*ax,*bx,*cx,u) 
     }      SHFT(*fa,*fb,*fc,fu) 
   #ifdef DEBUG
     wav[i]=mi;        printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
     if(mi==0)        fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  #endif
   }    } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
   } 
   for(i=1; i<=imx; i++){  
     for(mi=1; mi<wav[i];mi++){  /*************** linmin ************************/
       if (stepm <=0)  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
         dh[mi][i]=1;  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
       else{  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
         if (s[mw[mi+1][i]][i] > nlstate) {  the value of func at the returned location p . This is actually all accomplished by calling the
           if (agedc[i] < 2*AGESUP) {  routines mnbrak and brent .*/
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  int ncom; 
           if(j==0) j=1;  /* Survives at least one month after exam */  double *pcom,*xicom;
           k=k+1;  double (*nrfunc)(double []); 
           if (j >= jmax) jmax=j;   
           if (j <= jmin) jmin=j;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
           sum=sum+j;  { 
           /* if (j<10) printf("j=%d num=%d ",j,i); */    double brent(double ax, double bx, double cx, 
           }                 double (*f)(double), double tol, double *xmin); 
         }    double f1dim(double x); 
         else{    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));                double *fc, double (*func)(double)); 
           k=k+1;    int j; 
           if (j >= jmax) jmax=j;    double xx,xmin,bx,ax; 
           else if (j <= jmin)jmin=j;    double fx,fb,fa;
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */   
           sum=sum+j;    ncom=n; 
         }    pcom=vector(1,n); 
         jk= j/stepm;    xicom=vector(1,n); 
         jl= j -jk*stepm;    nrfunc=func; 
         ju= j -(jk+1)*stepm;    for (j=1;j<=n;j++) { 
         if(jl <= -ju)      pcom[j]=p[j]; 
           dh[mi][i]=jk;      xicom[j]=xi[j]; 
         else    } 
           dh[mi][i]=jk+1;    ax=0.0; 
         if(dh[mi][i]==0)    xx=1.0; 
           dh[mi][i]=1; /* At least one step */    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
       }    *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);
   jmean=sum/k;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  #endif
  }    for (j=1;j<=n;j++) { 
 /*********** Tricode ****************************/      xi[j] *= xmin; 
 void tricode(int *Tvar, int **nbcode, int imx)      p[j] += xi[j]; 
 {    } 
   int Ndum[20],ij=1, k, j, i;    free_vector(xicom,1,n); 
   int cptcode=0;    free_vector(pcom,1,n); 
   cptcoveff=0;  } 
    
   for (k=0; k<19; k++) Ndum[k]=0;  
   for (k=1; k<=7; k++) ncodemax[k]=0;  /*************** powell ************************/
   /*
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  Minimization of a function func of n variables. Input consists of an initial starting point
     for (i=1; i<=imx; i++) {  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
       ij=(int)(covar[Tvar[j]][i]);  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
       Ndum[ij]++;  such that failure to decrease by more than this amount on one iteration signals doneness. On
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
       if (ij > cptcode) cptcode=ij;  function value at p , and iter is the number of iterations taken. The routine linmin is used.
     }   */
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     for (i=0; i<=cptcode; i++) {              double (*func)(double [])) 
       if(Ndum[i]!=0) ncodemax[j]++;  { 
     }    void linmin(double p[], double xi[], int n, double *fret, 
     ij=1;                double (*func)(double [])); 
     int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
     for (i=1; i<=ncodemax[j]; i++) {    double directest;
       for (k=0; k<=19; k++) {    double fp,fptt;
         if (Ndum[k] != 0) {    double *xits;
           nbcode[Tvar[j]][ij]=k;    int niterf, itmp;
           ij++;  
         }    pt=vector(1,n); 
         if (ij > ncodemax[j]) break;    ptt=vector(1,n); 
       }      xit=vector(1,n); 
     }    xits=vector(1,n); 
   }      *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
  for (k=0; k<19; k++) Ndum[k]=0;      rcurr_time = time(NULL);  
     for (*iter=1;;++(*iter)) { 
  for (i=1; i<=ncovmodel-2; i++) {      fp=(*fret); 
       ij=Tvar[i];      ibig=0; 
       Ndum[ij]++;      del=0.0; 
     }      rlast_time=rcurr_time;
       /* (void) gettimeofday(&curr_time,&tzp); */
  ij=1;      rcurr_time = time(NULL);  
  for (i=1; i<=10; i++) {      curr_time = *localtime(&rcurr_time);
    if((Ndum[i]!=0) && (i<=ncov)){      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
      Tvaraff[ij]=i;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
      ij++;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
    }     for (i=1;i<=n;i++) {
  }        printf(" %d %.12f",i, p[i]);
          fprintf(ficlog," %d %.12lf",i, p[i]);
     cptcoveff=ij-1;        fprintf(ficrespow," %.12lf", p[i]);
 }      }
       printf("\n");
 /*********** Health Expectancies ****************/      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");fflush(ficrespow);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)      if(*iter <=3){
 {        tml = *localtime(&rcurr_time);
   /* Health expectancies */        strcpy(strcurr,asctime(&tml));
   int i, j, nhstepm, hstepm, h;        rforecast_time=rcurr_time; 
   double age, agelim,hf;        itmp = strlen(strcurr);
   double ***p3mat;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
            strcurr[itmp-1]='\0';
   fprintf(ficreseij,"# Health expectancies\n");        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
   fprintf(ficreseij,"# Age");        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
   for(i=1; i<=nlstate;i++)        for(niterf=10;niterf<=30;niterf+=10){
     for(j=1; j<=nlstate;j++)          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
       fprintf(ficreseij," %1d-%1d",i,j);          forecast_time = *localtime(&rforecast_time);
   fprintf(ficreseij,"\n");          strcpy(strfor,asctime(&forecast_time));
           itmp = strlen(strfor);
   hstepm=1*YEARM; /*  Every j years of age (in month) */          if(strfor[itmp-1]=='\n')
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          strfor[itmp-1]='\0';
           printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
   agelim=AGESUP;          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        }
     /* nhstepm age range expressed in number of stepm */      }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);      for (i=1;i<=n;i++) { 
     /* Typically if 20 years = 20*12/6=40 stepm */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     if (stepm >= YEARM) hstepm=1;        fptt=(*fret); 
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */  #ifdef DEBUG
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  #endif
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); /* xit[n] has been loaded for direction i */
     for(i=1; i<=nlstate;i++)        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions 
       for(j=1; j<=nlstate;j++)                                         because that direction will be replaced unless the gain del is small
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){                                        in comparison with the 'probable' gain, mu^2, with the last average direction.
           eij[i][j][(int)age] +=(p3mat[i][j][h]+p3mat[i][j][h+1])/2.0;                                        Unless the n directions are conjugate some gain in the determinant may be obtained
         }                                        with the new direction.
                                            */
     hf=1;          del=fabs(fptt-(*fret)); 
     if (stepm >= YEARM) hf=stepm/YEARM;          ibig=i; 
         } 
     for(i=1; i<=nlstate;i++)  #ifdef DEBUG
       for(j=1; j<=nlstate;j++){        printf("%d %.12e",i,(*fret));
         if (j==i) eij[i][j][(int)age]= (eij[i][j][(int)age]-0.5*stepm/12./hf);        fprintf(ficlog,"%d %.12e",i,(*fret));
         }        for (j=1;j<=n;j++) {
           xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     fprintf(ficreseij,"%3.0f",age );          printf(" x(%d)=%.12e",j,xit[j]);
     for(i=1; i<=nlstate;i++)          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       for(j=1; j<=nlstate;j++){        }
         fprintf(ficreseij," %9.4f", hf*eij[i][j][(int)age]);        for(j=1;j<=n;j++) {
       }          printf(" p(%d)=%.12e",j,p[j]);
     fprintf(ficreseij,"\n");          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
   }        printf("\n");
 }        fprintf(ficlog,"\n");
   #endif
 /************ Variance ******************/      } /* end i */
 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)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
 {  #ifdef DEBUG
   /* Variance of health expectancies */        int k[2],l;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        k[0]=1;
   double **newm;        k[1]=-1;
   double **dnewm,**doldm;        printf("Max: %.12e",(*func)(p));
   int i, j, nhstepm, hstepm, h;        fprintf(ficlog,"Max: %.12e",(*func)(p));
   int k, cptcode;        for (j=1;j<=n;j++) {
   double *xp;          printf(" %.12e",p[j]);
   double **gp, **gm;          fprintf(ficlog," %.12e",p[j]);
   double ***gradg, ***trgradg;        }
   double ***p3mat;        printf("\n");
   double age,agelim;        fprintf(ficlog,"\n");
   int theta;        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
    fprintf(ficresvij,"# Covariances of life expectancies\n");            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   fprintf(ficresvij,"# Age");            printf("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<=nlstate;i++)            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(j=1; j<=nlstate;j++)          }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   fprintf(ficresvij,"\n");          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
   xp=vector(1,npar);  #endif
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);  
          free_vector(xit,1,n); 
   hstepm=1*YEARM; /* Every year of age */        free_vector(xits,1,n); 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        free_vector(ptt,1,n); 
   agelim = AGESUP;        free_vector(pt,1,n); 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        return; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      } 
     if (stepm >= YEARM) hstepm=1;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        ptt[j]=2.0*p[j]-pt[j]; 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        xit[j]=p[j]-pt[j]; 
     gp=matrix(0,nhstepm,1,nlstate);        pt[j]=p[j]; 
     gm=matrix(0,nhstepm,1,nlstate);      } 
       fptt=(*func)(ptt); /* f_3 */
     for(theta=1; theta <=npar; theta++){      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
       for(i=1; i<=npar; i++){ /* Computes gradient */        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
       }        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
         /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
       if (popbased==1) {        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
         for(i=1; i<=nlstate;i++)  #ifdef NRCORIGINAL
           prlim[i][i]=probs[(int)age][i][ij];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
       }  #else
          t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
       for(j=1; j<= nlstate; j++){        t= t- del*SQR(fp-fptt);
         for(h=0; h<=nhstepm; h++){  #endif
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  #ifdef DEBUG
         }        printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
       }        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
            printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
       for(i=1; i<=npar; i++) /* Computes gradient */               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                 (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        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);
          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);
       if (popbased==1) {  #endif
         for(i=1; i<=nlstate;i++)  #ifdef POWELLORIGINAL
           prlim[i][i]=probs[(int)age][i][ij];        if (t < 0.0) { /* Then we use it for new direction */
       }  #else
         if (directest*t < 0.0) { /* Contradiction between both tests */
       for(j=1; j<= nlstate; j++){        printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
         for(h=0; h<=nhstepm; h++){        printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
         }      } 
       }        if (directest < 0.0) { /* Then we use it for new direction */
   #endif
       for(j=1; j<= nlstate; j++)          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
         for(h=0; h<=nhstepm; h++){          for (j=1;j<=n;j++) { 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
         }            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
     } /* End theta */          }
           printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   
     for(h=0; h<=nhstepm; h++)  #ifdef DEBUG
       for(j=1; j<=nlstate;j++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         for(theta=1; theta <=npar; theta++)          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           trgradg[h][j][theta]=gradg[h][theta][j];          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
     for(i=1;i<=nlstate;i++)            fprintf(ficlog," %.12e",xit[j]);
       for(j=1;j<=nlstate;j++)          }
         vareij[i][j][(int)age] =0.;          printf("\n");
     for(h=0;h<=nhstepm;h++){          fprintf(ficlog,"\n");
       for(k=0;k<=nhstepm;k++){  #endif
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        } /* end of t negative */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      } /* end if (fptt < fp)  */
         for(i=1;i<=nlstate;i++)    } 
           for(j=1;j<=nlstate;j++)  } 
             vareij[i][j][(int)age] += doldm[i][j];  
       }  /**** Prevalence limit (stable or period prevalence)  ****************/
     }  
     h=1;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     if (stepm >= YEARM) h=stepm/YEARM;  {
     fprintf(ficresvij,"%.0f ",age );    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     for(i=1; i<=nlstate;i++)       matrix by transitions matrix until convergence is reached */
       for(j=1; j<=nlstate;j++){    
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    int i, ii,j,k;
       }    double min, max, maxmin, maxmax,sumnew=0.;
     fprintf(ficresvij,"\n");    /* double **matprod2(); */ /* test */
     free_matrix(gp,0,nhstepm,1,nlstate);    double **out, cov[NCOVMAX+1], **pmij();
     free_matrix(gm,0,nhstepm,1,nlstate);    double **newm;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    double agefin, delaymax=50 ; /* Max number of years to converge */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (ii=1;ii<=nlstate+ndeath;ii++)
   } /* End age */      for (j=1;j<=nlstate+ndeath;j++){
          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(xp,1,npar);      }
   free_matrix(doldm,1,nlstate,1,npar);    
   free_matrix(dnewm,1,nlstate,1,nlstate);    cov[1]=1.;
     
 }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 /************ Variance of prevlim ******************/      newm=savm;
 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)      /* Covariates have to be included here again */
 {      cov[2]=agefin;
   /* Variance of prevalence limit */      
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      for (k=1; k<=cptcovn;k++) {
   double **newm;        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double **dnewm,**doldm;        /*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]]);*/
   int i, j, nhstepm, hstepm;      }
   int k, cptcode;      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   double *xp;      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
   double *gp, *gm;      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
   double **gradg, **trgradg;      
   double age,agelim;      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   int theta;      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
          /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   fprintf(ficresvpl,"# Age");      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
   for(i=1; i<=nlstate;i++)      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
       fprintf(ficresvpl," %1d-%1d",i,i);      
   fprintf(ficresvpl,"\n");      savm=oldm;
       oldm=newm;
   xp=vector(1,npar);      maxmax=0.;
   dnewm=matrix(1,nlstate,1,npar);      for(j=1;j<=nlstate;j++){
   doldm=matrix(1,nlstate,1,nlstate);        min=1.;
          max=0.;
   hstepm=1*YEARM; /* Every year of age */        for(i=1; i<=nlstate; i++) {
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          sumnew=0;
   agelim = AGESUP;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          prlim[i][j]= newm[i][j]/(1-sumnew);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
     if (stepm >= YEARM) hstepm=1;          max=FMAX(max,prlim[i][j]);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          min=FMIN(min,prlim[i][j]);
     gradg=matrix(1,npar,1,nlstate);        }
     gp=vector(1,nlstate);        maxmin=max-min;
     gm=vector(1,nlstate);        maxmax=FMAX(maxmax,maxmin);
       } /* j loop */
     for(theta=1; theta <=npar; theta++){      if(maxmax < ftolpl){
       for(i=1; i<=npar; i++){ /* Computes gradient */        return prlim;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      }
       }    } /* age loop */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    return prlim; /* should not reach here */
       for(i=1;i<=nlstate;i++)  }
         gp[i] = prlim[i][i];  
      /*************** transition probabilities ***************/ 
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  {
       for(i=1;i<=nlstate;i++)    /* According to parameters values stored in x and the covariate's values stored in cov,
         gm[i] = prlim[i][i];       computes the probability to be observed in state j being in state i by appying the
        model to the ncovmodel covariates (including constant and age).
       for(i=1;i<=nlstate;i++)       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
     } /* End theta */       ncth covariate in the global vector x is given by the formula:
        j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
     trgradg =matrix(1,nlstate,1,npar);       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
        Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
     for(j=1; j<=nlstate;j++)       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
       for(theta=1; theta <=npar; theta++)       Outputs ps[i][j] the probability to be observed in j being in j according to
         trgradg[j][theta]=gradg[theta][j];       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     */
     for(i=1;i<=nlstate;i++)    double s1, lnpijopii;
       varpl[i][(int)age] =0.;    /*double t34;*/
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    int i,j, nc, ii, jj;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  
     for(i=1;i<=nlstate;i++)      for(i=1; i<= nlstate; i++){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        for(j=1; j<i;j++){
           for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     fprintf(ficresvpl,"%.0f ",age );            /*lnpijopii += param[i][j][nc]*cov[nc];*/
     for(i=1; i<=nlstate;i++)            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     fprintf(ficresvpl,"\n");          }
     free_vector(gp,1,nlstate);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     free_vector(gm,1,nlstate);  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     free_matrix(gradg,1,npar,1,nlstate);        }
     free_matrix(trgradg,1,nlstate,1,npar);        for(j=i+1; j<=nlstate+ndeath;j++){
   } /* End age */          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];*/
   free_vector(xp,1,npar);            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   free_matrix(doldm,1,nlstate,1,npar);  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
   free_matrix(dnewm,1,nlstate,1,nlstate);          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
 }        }
       }
 /************ Variance of one-step probabilities  ******************/      
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      for(i=1; i<= nlstate; i++){
 {        s1=0;
   int i, j;        for(j=1; j<i; j++){
   int k=0, cptcode;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   double **dnewm,**doldm;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   double *xp;        }
   double *gp, *gm;        for(j=i+1; j<=nlstate+ndeath; j++){
   double **gradg, **trgradg;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   double age,agelim, cov[NCOVMAX];          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   int theta;        }
   char fileresprob[FILENAMELENGTH];        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
         ps[i][i]=1./(s1+1.);
   strcpy(fileresprob,"prob");        /* Computing other pijs */
   strcat(fileresprob,fileres);        for(j=1; j<i; j++)
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          ps[i][j]= exp(ps[i][j])*ps[i][i];
     printf("Problem with resultfile: %s\n", fileresprob);        for(j=i+1; j<=nlstate+ndeath; j++)
   }          ps[i][j]= exp(ps[i][j])*ps[i][i];
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
        } /* end i */
       
   xp=vector(1,npar);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for(jj=1; jj<= nlstate+ndeath; jj++){
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          ps[ii][jj]=0;
            ps[ii][ii]=1;
   cov[1]=1;        }
   for (age=bage; age<=fage; age ++){      }
     cov[2]=age;      
     gradg=matrix(1,npar,1,9);      
     trgradg=matrix(1,9,1,npar);      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
          /*   } */
     for(theta=1; theta <=npar; theta++){      /*   printf("\n "); */
       for(i=1; i<=npar; i++)      /* } */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      /* printf("\n ");printf("%lf ",cov[2]);*/
            /*
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        for(i=1; i<= npar; i++) printf("%f ",x[i]);
            goto end;*/
       k=0;      return ps;
       for(i=1; i<= (nlstate+ndeath); i++){  }
         for(j=1; j<=(nlstate+ndeath);j++){  
            k=k+1;  /**************** Product of 2 matrices ******************/
           gp[k]=pmmij[i][j];  
         }  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
       }  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       for(i=1; i<=npar; i++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    /* in, b, out are matrice of pointers which should have been initialized 
           before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    int i, j, k;
       k=0;    for(i=nrl; i<= nrh; i++)
       for(i=1; i<=(nlstate+ndeath); i++){      for(k=ncolol; k<=ncoloh; k++){
         for(j=1; j<=(nlstate+ndeath);j++){        out[i][k]=0.;
           k=k+1;        for(j=ncl; j<=nch; j++)
           gm[k]=pmmij[i][j];          out[i][k] +=in[i][j]*b[j][k];
         }      }
       }    return out;
        }
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    
     }  /************* Higher Matrix Product ***************/
   
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       for(theta=1; theta <=npar; theta++)  {
       trgradg[j][theta]=gradg[theta][j];    /* Computes the transition matrix starting at age 'age' over 
         'nhstepm*hstepm*stepm' months (i.e. until
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);       nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
      pmij(pmmij,cov,ncovmodel,x,nlstate);       (typically every 2 years instead of every month which is too big 
        for the memory).
      k=0;       Model is determined by parameters x and covariates have to be 
      for(i=1; i<=(nlstate+ndeath); i++){       included manually here. 
        for(j=1; j<=(nlstate+ndeath);j++){  
          k=k+1;       */
          gm[k]=pmmij[i][j];  
         }    int i, j, d, h, k;
      }    double **out, cov[NCOVMAX+1];
          double **newm;
      /*printf("\n%d ",(int)age);  
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    /* Hstepm could be zero and should return the unit matrix */
            for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        oldm[i][j]=(i==j ? 1.0 : 0.0);
      }*/        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
   fprintf(ficresprob,"\n%d ",(int)age);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      for(d=1; d <=hstepm; d++){
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        newm=savm;
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        /* Covariates have to be included here again */
   }        cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        for (k=1; k<=cptcovn;k++) 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for (k=1; k<=cptcovage;k++)
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 }        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
  free_vector(xp,1,npar);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 fclose(ficresprob);  
   
 }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
 /******************* Printing html file ***********/        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   int jj1, k1, i1, cpt;        savm=oldm;
   FILE *fichtm;        oldm=newm;
   /*char optionfilehtm[FILENAMELENGTH];*/      }
       for(i=1; i<=nlstate+ndeath; i++)
   strcpy(optionfilehtm,optionfile);        for(j=1;j<=nlstate+ndeath;j++) {
   strcat(optionfilehtm,".htm");          po[i][j][h]=newm[i][j];
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
     printf("Problem with %s \n",optionfilehtm), exit(0);        }
   }      /*printf("h=%d ",h);*/
     } /* end h */
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71 </font> <hr size=\"2\" color=\"#EC5E5E\">  /*     printf("\n H=%d \n",h); */
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    return po;
   }
 Total number of observations=%d <br>  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  #ifdef NLOPT
 <hr  size=\"2\" color=\"#EC5E5E\">    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
 <li>Outputs files<br><br>\n    double fret;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    double *xt;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    int j;
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    myfunc_data *d2 = (myfunc_data *) pd;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>  /* xt = (p1-1); */
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    xt=vector(1,n); 
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>  
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>    printf("Function = %.12lf ",fret);
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    printf("\n");
     free_vector(xt,1,n);
 fprintf(fichtm," <li>Graphs</li><p>");    return fret;
   }
  m=cptcoveff;  #endif
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
   /*************** log-likelihood *************/
  jj1=0;  double func( double *x)
  for(k1=1; k1<=m;k1++){  {
    for(i1=1; i1<=ncodemax[k1];i1++){    int i, ii, j, k, mi, d, kk;
        jj1++;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
        if (cptcovn > 0) {    double **out;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    double sw; /* Sum of weights */
          for (cpt=1; cpt<=cptcoveff;cpt++)    double lli; /* Individual log likelihood */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    int s1, s2;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    double bbh, survp;
        }    long ipmx;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    /*extern weight */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        /* We are differentiating ll according to initial status */
        for(cpt=1; cpt<nlstate;cpt++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    /*for(i=1;i<imx;i++) 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      printf(" %d\n",s[4][i]);
        }    */
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    ++countcallfunc;
 interval) in state (%d): v%s%d%d.gif <br>  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      cov[1]=1.;
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {    for(k=1; k<=nlstate; k++) ll[k]=0.;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    if(mle==1){
      }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        /* Computes the values of the ncovmodel covariates of the model
 health expectancies in states (1) and (2): e%s%d.gif<br>           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
 fprintf(fichtm,"\n</body>");           to be observed in j being in i according to the model.
    }         */
    }        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
 fclose(fichtm);          cov[2+k]=covar[Tvar[k]][i];
 }        }
         /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
 /******************* Gnuplot file **************/           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){           has been calculated etc */
         for(mi=1; mi<= wav[i]-1; mi++){
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   strcpy(optionfilegnuplot,optionfilefiname);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcat(optionfilegnuplot,".plt");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {            }
     printf("Problem with file %s",optionfilegnuplot);          for(d=0; d<dh[mi][i]; d++){
   }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 #ifdef windows            for (kk=1; kk<=cptcovage;kk++) {
     fprintf(ficgp,"cd \"%s\" \n",pathc);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
 #endif            }
 m=pow(2,cptcoveff);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
  /* 1eme*/            savm=oldm;
   for (cpt=1; cpt<= nlstate ; cpt ++) {            oldm=newm;
    for (k1=1; k1<= m ; k1 ++) {          } /* end mult */
         
 #ifdef windows          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     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);          /* But now since version 0.9 we anticipate for bias at large stepm.
 #endif           * If stepm is larger than one month (smallest stepm) and if the exact delay 
 #ifdef unix           * (in months) between two waves is not a multiple of stepm, we rounded to 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);           * the nearest (and in case of equal distance, to the lowest) interval but now
 #endif           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
 for (i=1; i<= nlstate ; i ++) {           * probability in order to take into account the bias as a fraction of the way
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   else fprintf(ficgp," \%%*lf (\%%*lf)");           * -stepm/2 to stepm/2 .
 }           * For stepm=1 the results are the same as for previous versions of Imach.
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);           * For stepm > 1 the results are less biased than in previous versions. 
     for (i=1; i<= nlstate ; i ++) {           */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          s1=s[mw[mi][i]][i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");          s2=s[mw[mi+1][i]][i];
 }          bbh=(double)bh[mi][i]/(double)stepm; 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          /* bias bh is positive if real duration
      for (i=1; i<= nlstate ; i ++) {           * is higher than the multiple of stepm and negative otherwise.
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");           */
   else fprintf(ficgp," \%%*lf (\%%*lf)");          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 }            if( s2 > nlstate){ 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            /* i.e. if s2 is a death state and if the date of death is known 
 #ifdef unix               then the contribution to the likelihood is the probability to 
 fprintf(ficgp,"\nset ter gif small size 400,300");               die between last step unit time and current  step unit time, 
 #endif               which is also equal to probability to die before dh 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);               minus probability to die before dh-stepm . 
    }               In version up to 0.92 likelihood was computed
   }          as if date of death was unknown. Death was treated as any other
   /*2 eme*/          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
   for (k1=1; k1<= m ; k1 ++) {          to consider that at each interview the state was recorded
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          (healthy, disable or death) and IMaCh was corrected; but when we
              introduced the exact date of death then we should have modified
     for (i=1; i<= nlstate+1 ; i ++) {          the contribution of an exact death to the likelihood. This new
       k=2*i;          contribution is smaller and very dependent of the step unit
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          stepm. It is no more the probability to die between last interview
       for (j=1; j<= nlstate+1 ; j ++) {          and month of death but the probability to survive from last
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          interview up to one month before death multiplied by the
   else fprintf(ficgp," \%%*lf (\%%*lf)");          probability to die within a month. Thanks to Chris
 }            Jackson for correcting this bug.  Former versions increased
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          mortality artificially. The bad side is that we add another loop
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          which slows down the processing. The difference can be up to 10%
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          lower mortality.
       for (j=1; j<= nlstate+1 ; j ++) {            */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          /* If, at the beginning of the maximization mostly, the
         else fprintf(ficgp," \%%*lf (\%%*lf)");             cumulative probability or probability to be dead is
 }               constant (ie = 1) over time d, the difference is equal to
       fprintf(ficgp,"\" t\"\" w l 0,");             0.  out[s1][3] = savm[s1][3]: probability, being at state
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);             s1 at precedent wave, to be dead a month before current
       for (j=1; j<= nlstate+1 ; j ++) {             wave is equal to probability, being at state s1 at
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");             precedent wave, to be dead at mont of the current
   else fprintf(ficgp," \%%*lf (\%%*lf)");             wave. Then the observed probability (that this person died)
 }               is null according to current estimated parameter. In fact,
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");             it should be very low but not zero otherwise the log go to
       else fprintf(ficgp,"\" t\"\" w l 0,");             infinity.
     }          */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  /* #ifdef INFINITYORIGINAL */
   }  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
    /* #else */
   /*3eme*/  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
   /*          lli=log(mytinydouble); */
   for (k1=1; k1<= m ; k1 ++) {  /*        else */
     for (cpt=1; cpt<= nlstate ; cpt ++) {  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
       k=2+nlstate*(cpt-1);  /* #endif */
       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);              lli=log(out[s1][s2] - savm[s1][s2]);
       for (i=1; i< nlstate ; i ++) {  
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          } else if  (s2==-2) {
       }            for (j=1,survp=0. ; j<=nlstate; j++) 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     }            /*survp += out[s1][j]; */
     }            lli= log(survp);
            }
   /* CV preval stat */          
     for (k1=1; k1<= m ; k1 ++) {          else if  (s2==-4) { 
     for (cpt=1; cpt<nlstate ; cpt ++) {            for (j=3,survp=0. ; j<=nlstate; j++)  
       k=3;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       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/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);            lli= log(survp); 
           } 
       for (i=1; i< nlstate ; i ++)  
         fprintf(ficgp,"+$%d",k+i+1);          else if  (s2==-5) { 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            for (j=1,survp=0. ; j<=2; j++)  
                    survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       l=3+(nlstate+ndeath)*cpt;            lli= log(survp); 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          } 
       for (i=1; i< nlstate ; i ++) {          
         l=3+(nlstate+ndeath)*cpt;          else{
         fprintf(ficgp,"+$%d",l+i+1);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            } 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     }          /*if(lli ==000.0)*/
   }            /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
            ipmx +=1;
   /* proba elementaires */          sw += weight[i];
    for(i=1,jk=1; i <=nlstate; i++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(k=1; k <=(nlstate+ndeath); k++){          /* if (lli < log(mytinydouble)){ */
       if (k != i) {          /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
         for(j=1; j <=ncovmodel; j++){          /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
                  /* } */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        } /* end of wave */
           jk++;      } /* end of individual */
           fprintf(ficgp,"\n");    }  else if(mle==2){
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
     for(jk=1; jk <=m; jk++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    i=1;            }
    for(k2=1; k2<=nlstate; k2++) {          for(d=0; d<=dh[mi][i]; d++){
      k3=i;            newm=savm;
      for(k=1; k<=(nlstate+ndeath); k++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
        if (k != k2){            for (kk=1; kk<=cptcovage;kk++) {
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 ij=1;            }
         for(j=3; j <=ncovmodel; j++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            savm=oldm;
             ij++;            oldm=newm;
           }          } /* end mult */
           else        
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
           fprintf(ficgp,")/(1");          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 */
         for(k1=1; k1 <=nlstate; k1++){            ipmx +=1;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          sw += weight[i];
 ij=1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for(j=3; j <=ncovmodel; j++){        } /* end of wave */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      } /* end of individual */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    }  else if(mle==3){  /* exponential inter-extrapolation */
             ij++;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           else        for(mi=1; mi<= wav[i]-1; mi++){
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          for (ii=1;ii<=nlstate+ndeath;ii++)
           }            for (j=1;j<=nlstate+ndeath;j++){
           fprintf(ficgp,")");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);            }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          for(d=0; d<dh[mi][i]; d++){
         i=i+ncovmodel;            newm=savm;
        }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      }            for (kk=1; kk<=cptcovage;kk++) {
    }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            }
    }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                             1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fclose(ficgp);            savm=oldm;
 }  /* end gnuplot */            oldm=newm;
           } /* end mult */
         
 /*************** Moving average **************/          s1=s[mw[mi][i]][i];
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   int i, cpt, cptcod;          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 */
     for (agedeb=agemin; agedeb<=fage; agedeb++)          ipmx +=1;
       for (i=1; i<=nlstate;i++)          sw += weight[i];
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           mobaverage[(int)agedeb][i][cptcod]=0.;        } /* end of wave */
          } /* end of individual */
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       for (i=1; i<=nlstate;i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           for (cpt=0;cpt<=4;cpt++){        for(mi=1; mi<= wav[i]-1; mi++){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          for (ii=1;ii<=nlstate+ndeath;ii++)
           }            for (j=1;j<=nlstate+ndeath;j++){
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
     }          for(d=0; d<dh[mi][i]; d++){
                newm=savm;
 }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 /************** Forecasting ******************/            }
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int *popage;            savm=oldm;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            oldm=newm;
   double *popeffectif,*popcount;          } /* end mult */
   double ***p3mat;        
   char fileresf[FILENAMELENGTH];          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
  agelim=AGESUP;          if( s2 > nlstate){ 
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            }
            ipmx +=1;
   strcpy(fileresf,"f");          sw += weight[i];
   strcat(fileresf,fileres);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   if((ficresf=fopen(fileresf,"w"))==NULL) {  /*      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]); */
     printf("Problem with forecast resultfile: %s\n", fileresf);        } /* end of wave */
   }      } /* end of individual */
   printf("Computing forecasting: result on file '%s' \n", fileresf);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   if (mobilav==1) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for (j=1;j<=nlstate+ndeath;j++){
     movingaverage(agedeb, fage, agemin, mobaverage);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for(d=0; d<dh[mi][i]; d++){
   if (stepm<=12) stepsize=1;            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   agelim=AGESUP;            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   hstepm=1;            }
   hstepm=hstepm/stepm;          
   yp1=modf(dateintmean,&yp);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   anprojmean=yp;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   yp2=modf((yp1*12),&yp);            savm=oldm;
   mprojmean=yp;            oldm=newm;
   yp1=modf((yp2*30.5),&yp);          } /* end mult */
   jprojmean=yp;        
   if(jprojmean==0) jprojmean=1;          s1=s[mw[mi][i]][i];
   if(mprojmean==0) jprojmean=1;          s2=s[mw[mi+1][i]][i];
            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);          ipmx +=1;
            sw += weight[i];
   for(cptcov=1;cptcov<=i2;cptcov++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          /*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]);*/
       k=k+1;        } /* end of wave */
       fprintf(ficresf,"\n#******");      } /* end of individual */
       for(j=1;j<=cptcoveff;j++) {    } /* End of if */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       fprintf(ficresf,"******\n");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       fprintf(ficresf,"# StartingAge FinalAge");    return -l;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  }
        
        /*************** log-likelihood *************/
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  double funcone( double *x)
         fprintf(ficresf,"\n");  {
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      /* Same as likeli but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    double **out;
           nhstepm = nhstepm/hstepm;    double lli; /* Individual log likelihood */
              double llt;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int s1, s2;
           oldm=oldms;savm=savms;    double bbh, survp;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /*extern weight */
            /* We are differentiating ll according to initial status */
           for (h=0; h<=nhstepm; h++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
             if (h==(int) (calagedate+YEARM*cpt)) {    /*for(i=1;i<imx;i++) 
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);      printf(" %d\n",s[4][i]);
             }    */
             for(j=1; j<=nlstate+ndeath;j++) {    cov[1]=1.;
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                  for(k=1; k<=nlstate; k++) ll[k]=0.;
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                 else {      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      for(mi=1; mi<= wav[i]-1; mi++){
                 }        for (ii=1;ii<=nlstate+ndeath;ii++)
                          for (j=1;j<=nlstate+ndeath;j++){
               }            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               if (h==(int)(calagedate+12*cpt)){            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                 fprintf(ficresf," %.3f", kk1);          }
                                for(d=0; d<dh[mi][i]; d++){
               }          newm=savm;
             }          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           }          for (kk=1; kk<=cptcovage;kk++) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }          }
       }          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     }          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                  /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
           savm=oldm;
   fclose(ficresf);          oldm=newm;
 }        } /* end mult */
 /************** Forecasting ******************/        
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){        s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        bbh=(double)bh[mi][i]/(double)stepm; 
   int *popage;        /* bias is positive if real duration
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;         * is higher than the multiple of stepm and negative otherwise.
   double *popeffectif,*popcount;         */
   double ***p3mat,***tabpop,***tabpopprev;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   char filerespop[FILENAMELENGTH];          lli=log(out[s1][s2] - savm[s1][s2]);
         } else if  (s2==-2) {
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (j=1,survp=0. ; j<=nlstate; j++) 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   agelim=AGESUP;          lli= log(survp);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;        }else if (mle==1){
            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        } else if(mle==2){
            lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
          } else if(mle==3){  /* exponential inter-extrapolation */
   strcpy(filerespop,"pop");          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 */
   strcat(filerespop,fileres);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          lli=log(out[s1][s2]); /* Original formula */
     printf("Problem with forecast resultfile: %s\n", filerespop);        } else{  /* mle=0 back to 1 */
   }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   printf("Computing forecasting: result on file '%s' \n", filerespop);          /*lli=log(out[s1][s2]); */ /* Original formula */
         } /* End of if */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        ipmx +=1;
         sw += weight[i];
   if (mobilav==1) {        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        /*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]); */
     movingaverage(agedeb, fage, agemin, mobaverage);        if(globpr){
   }          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
    %11.6f %11.6f %11.6f ", \
   stepsize=(int) (stepm+YEARM-1)/YEARM;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   if (stepm<=12) stepsize=1;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
            for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   agelim=AGESUP;            llt +=ll[k]*gipmx/gsw;
              fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   hstepm=1;          }
   hstepm=hstepm/stepm;          fprintf(ficresilk," %10.6f\n", -llt);
          }
   if (popforecast==1) {      } /* end of wave */
     if((ficpop=fopen(popfile,"r"))==NULL) {    } /* end of individual */
       printf("Problem with population file : %s\n",popfile);exit(0);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     popage=ivector(0,AGESUP);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     popeffectif=vector(0,AGESUP);    if(globpr==0){ /* First time we count the contributions and weights */
     popcount=vector(0,AGESUP);      gipmx=ipmx;
          gsw=sw;
     i=1;      }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    return -l;
      }
     imx=i;  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  
   }  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   for(cptcov=1;cptcov<=i2;cptcov++){  {
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    /* This routine should help understanding what is done with 
       k=k+1;       the selection of individuals/waves and
       fprintf(ficrespop,"\n#******");       to check the exact contribution to the likelihood.
       for(j=1;j<=cptcoveff;j++) {       Plotting could be done.
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     */
       }    int k;
       fprintf(ficrespop,"******\n");  
       fprintf(ficrespop,"# Age");    if(*globpri !=0){ /* Just counts and sums, no printings */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      strcpy(fileresilk,"ilk"); 
       if (popforecast==1)  fprintf(ficrespop," [Population]");      strcat(fileresilk,fileres);
            if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       for (cpt=0; cpt<=0;cpt++) {        printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
              }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      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");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
           nhstepm = nhstepm/hstepm;      /*  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++) 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
           oldm=oldms;savm=savms;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      }
          
           for (h=0; h<=nhstepm; h++){    *fretone=(*funcone)(p);
             if (h==(int) (calagedate+YEARM*cpt)) {    if(*globpri !=0){
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      fclose(ficresilk);
             }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
             for(j=1; j<=nlstate+ndeath;j++) {      fflush(fichtm); 
               kk1=0.;kk2=0;    } 
               for(i=1; i<=nlstate;i++) {                  return;
                 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];  /*********** Maximum Likelihood Estimation ***************/
                 }  
               }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
               if (h==(int)(calagedate+12*cpt)){  {
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    int i,j, iter=0;
                   /*fprintf(ficrespop," %.3f", kk1);    double **xi;
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    double fret;
               }    double fretone; /* Only one call to likelihood */
             }    /*  char filerespow[FILENAMELENGTH];*/
             for(i=1; i<=nlstate;i++){  
               kk1=0.;  #ifdef NLOPT
                 for(j=1; j<=nlstate;j++){    int creturn;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    nlopt_opt opt;
                 }    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    double *lb;
             }    double minf; /* the minimum objective value, upon return */
     double * p1; /* Shifted parameters from 0 instead of 1 */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    myfunc_data dinst, *d = &dinst;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  #endif
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }    xi=matrix(1,npar,1,npar);
       }    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++)
   /******/        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    strcpy(filerespow,"pow"); 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      strcat(filerespow,fileres);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){    if((ficrespow=fopen(filerespow,"w"))==NULL) {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      printf("Problem with resultfile: %s\n", filerespow);
           nhstepm = nhstepm/hstepm;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
              }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
           oldm=oldms;savm=savms;    for (i=1;i<=nlstate;i++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for(j=1;j<=nlstate+ndeath;j++)
           for (h=0; h<=nhstepm; h++){        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
             if (h==(int) (calagedate+YEARM*cpt)) {    fprintf(ficrespow,"\n");
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  #ifdef POWELL
             }    powell(p,xi,npar,ftol,&iter,&fret,func);
             for(j=1; j<=nlstate+ndeath;j++) {  #endif
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                #ifdef NLOPT
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      #ifdef NEWUOA
               }    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  #else
             }    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
           }  #endif
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    lb=vector(0,npar-1);
         }    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
       }    nlopt_set_lower_bounds(opt, lb);
    }    nlopt_set_initial_step1(opt, 0.1);
   }    
      p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    d->function = func;
     printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
   if (popforecast==1) {    nlopt_set_min_objective(opt, myfunc, d);
     free_ivector(popage,0,AGESUP);    nlopt_set_xtol_rel(opt, ftol);
     free_vector(popeffectif,0,AGESUP);    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
     free_vector(popcount,0,AGESUP);      printf("nlopt failed! %d\n",creturn); 
   }    }
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    else {
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
   fclose(ficrespop);      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
 }      iter=1; /* not equal */
     }
 /***********************************************/    nlopt_destroy(opt);
 /**************** Main Program *****************/  #endif
 /***********************************************/    free_matrix(xi,1,npar,1,npar);
     fclose(ficrespow);
 int main(int argc, char *argv[])    printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
 {    fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  
   double agedeb, agefin,hf;  }
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  
   /**** Computes Hessian and covariance matrix ***/
   double fret;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   double **xi,tmp,delta;  {
     double  **a,**y,*x,pd;
   double dum; /* Dummy variable */    double **hess;
   double ***p3mat;    int i, j;
   int *indx;    int *indx;
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    void lubksb(double **a, int npar, int *indx, double b[]) ;
      void ludcmp(double **a, int npar, int *indx, double *d) ;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    double gompertz(double p[]);
     hess=matrix(1,npar,1,npar);
   char filerest[FILENAMELENGTH];  
   char fileregp[FILENAMELENGTH];    printf("\nCalculation of the hessian matrix. Wait...\n");
   char popfile[FILENAMELENGTH];    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    for (i=1;i<=npar;i++){
   int firstobs=1, lastobs=10;      printf("%d",i);fflush(stdout);
   int sdeb, sfin; /* Status at beginning and end */      fprintf(ficlog,"%d",i);fflush(ficlog);
   int c,  h , cpt,l;     
   int ju,jl, mi;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      /*  printf(" %f ",p[i]);
   int mobilav=0,popforecast=0;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   int hstepm, nhstepm;    }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    
     for (i=1;i<=npar;i++) {
   double bage, fage, age, agelim, agebase;      for (j=1;j<=npar;j++)  {
   double ftolpl=FTOL;        if (j>i) { 
   double **prlim;          printf(".%d%d",i,j);fflush(stdout);
   double *severity;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   double ***param; /* Matrix of parameters */          hess[i][j]=hessij(p,delti,i,j,func,npar);
   double  *p;          
   double **matcov; /* Matrix of covariance */          hess[j][i]=hess[i][j];    
   double ***delti3; /* Scale */          /*printf(" %lf ",hess[i][j]);*/
   double *delti; /* Scale */        }
   double ***eij, ***vareij;      }
   double **varpl; /* Variances of prevalence limits by age */    }
   double *epj, vepp;    printf("\n");
   double kk1, kk2;    fprintf(ficlog,"\n");
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  
      printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   char version[80]="Imach version 0.71, February 2002, INED-EUROREVES ";    
   char *alph[]={"a","a","b","c","d","e"}, str[4];    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
     x=vector(1,npar);
   char z[1]="c", occ;    indx=ivector(1,npar);
 #include <sys/time.h>    for (i=1;i<=npar;i++)
 #include <time.h>      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    ludcmp(a,npar,indx,&pd);
    
   /* long total_usecs;    for (j=1;j<=npar;j++) {
   struct timeval start_time, end_time;      for (i=1;i<=npar;i++) x[i]=0;
        x[j]=1;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
   printf("\n%s",version);      }
   if(argc <=1){    }
     printf("\nEnter the parameter file name: ");  
     scanf("%s",pathtot);    printf("\n#Hessian matrix#\n");
   }    fprintf(ficlog,"\n#Hessian matrix#\n");
   else{    for (i=1;i<=npar;i++) { 
     strcpy(pathtot,argv[1]);      for (j=1;j<=npar;j++) { 
   }        printf("%.3e ",hess[i][j]);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        fprintf(ficlog,"%.3e ",hess[i][j]);
   /*cygwin_split_path(pathtot,path,optionfile);      }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      printf("\n");
   /* cutv(path,optionfile,pathtot,'\\');*/      fprintf(ficlog,"\n");
     }
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    /* Recompute Inverse */
   chdir(path);    for (i=1;i<=npar;i++)
   replace(pathc,path);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
 /*-------- arguments in the command line --------*/  
     /*  printf("\n#Hessian matrix recomputed#\n");
   strcpy(fileres,"r");  
   strcat(fileres, optionfilefiname);    for (j=1;j<=npar;j++) {
   strcat(fileres,".txt");    /* Other files have txt extension */      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
   /*---------arguments file --------*/      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        y[i][j]=x[i];
     printf("Problem with optionfile %s\n",optionfile);        printf("%.3e ",y[i][j]);
     goto end;        fprintf(ficlog,"%.3e ",y[i][j]);
   }      }
       printf("\n");
   strcpy(filereso,"o");      fprintf(ficlog,"\n");
   strcat(filereso,fileres);    }
   if((ficparo=fopen(filereso,"w"))==NULL) {    */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
   /* Reads comments: lines beginning with '#' */    free_vector(x,1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    free_ivector(indx,1,npar);
     ungetc(c,ficpar);    free_matrix(hess,1,npar,1,npar);
     fgets(line, MAXLINE, ficpar);  
     puts(line);  
     fputs(line,ficparo);  }
   }  
   ungetc(c,ficpar);  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   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);  {
   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);    int i;
   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);    int l=1, lmax=20;
 while((c=getc(ficpar))=='#' && c!= EOF){    double k1,k2;
     ungetc(c,ficpar);    double p2[MAXPARM+1]; /* identical to x */
     fgets(line, MAXLINE, ficpar);    double res;
     puts(line);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     fputs(line,ficparo);    double fx;
   }    int k=0,kmax=10;
   ungetc(c,ficpar);    double l1;
    
        fx=func(x);
   covar=matrix(0,NCOVMAX,1,n);    for (i=1;i<=npar;i++) p2[i]=x[i];
   cptcovn=0;    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      l1=pow(10,l);
       delts=delt;
   ncovmodel=2+cptcovn;      for(k=1 ; k <kmax; k=k+1){
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        delt = delta*(l1*k);
          p2[theta]=x[theta] +delt;
   /* Read guess parameters */        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
   /* Reads comments: lines beginning with '#' */        p2[theta]=x[theta]-delt;
   while((c=getc(ficpar))=='#' && c!= EOF){        k2=func(p2)-fx;
     ungetc(c,ficpar);        /*res= (k1-2.0*fx+k2)/delt/delt; */
     fgets(line, MAXLINE, ficpar);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     puts(line);        
     fputs(line,ficparo);  #ifdef DEBUGHESS
   }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   ungetc(c,ficpar);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
    #endif
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     for(i=1; i <=nlstate; i++)        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     for(j=1; j <=nlstate+ndeath-1; j++){          k=kmax;
       fscanf(ficpar,"%1d%1d",&i1,&j1);        }
       fprintf(ficparo,"%1d%1d",i1,j1);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       printf("%1d%1d",i,j);          k=kmax; l=lmax*10;
       for(k=1; k<=ncovmodel;k++){        }
         fscanf(ficpar," %lf",&param[i][j][k]);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         printf(" %lf",param[i][j][k]);          delts=delt;
         fprintf(ficparo," %lf",param[i][j][k]);        }
       }      }
       fscanf(ficpar,"\n");    }
       printf("\n");    delti[theta]=delts;
       fprintf(ficparo,"\n");    return res; 
     }    
    }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   p=param[1][1];  {
      int i;
   /* Reads comments: lines beginning with '#' */    int l=1, lmax=20;
   while((c=getc(ficpar))=='#' && c!= EOF){    double k1,k2,k3,k4,res,fx;
     ungetc(c,ficpar);    double p2[MAXPARM+1];
     fgets(line, MAXLINE, ficpar);    int k;
     puts(line);  
     fputs(line,ficparo);    fx=func(x);
   }    for (k=1; k<=2; k++) {
   ungetc(c,ficpar);      for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      k1=func(p2)-fx;
   for(i=1; i <=nlstate; i++){    
     for(j=1; j <=nlstate+ndeath-1; j++){      p2[thetai]=x[thetai]+delti[thetai]/k;
       fscanf(ficpar,"%1d%1d",&i1,&j1);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       printf("%1d%1d",i,j);      k2=func(p2)-fx;
       fprintf(ficparo,"%1d%1d",i1,j1);    
       for(k=1; k<=ncovmodel;k++){      p2[thetai]=x[thetai]-delti[thetai]/k;
         fscanf(ficpar,"%le",&delti3[i][j][k]);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         printf(" %le",delti3[i][j][k]);      k3=func(p2)-fx;
         fprintf(ficparo," %le",delti3[i][j][k]);    
       }      p2[thetai]=x[thetai]-delti[thetai]/k;
       fscanf(ficpar,"\n");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       printf("\n");      k4=func(p2)-fx;
       fprintf(ficparo,"\n");      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     }  #ifdef DEBUG
   }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   delti=delti3[1][1];      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
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    return res;
     ungetc(c,ficpar);  }
     fgets(line, MAXLINE, ficpar);  
     puts(line);  /************** Inverse of matrix **************/
     fputs(line,ficparo);  void ludcmp(double **a, int n, int *indx, double *d) 
   }  { 
   ungetc(c,ficpar);    int i,imax,j,k; 
      double big,dum,sum,temp; 
   matcov=matrix(1,npar,1,npar);    double *vv; 
   for(i=1; i <=npar; i++){   
     fscanf(ficpar,"%s",&str);    vv=vector(1,n); 
     printf("%s",str);    *d=1.0; 
     fprintf(ficparo,"%s",str);    for (i=1;i<=n;i++) { 
     for(j=1; j <=i; j++){      big=0.0; 
       fscanf(ficpar," %le",&matcov[i][j]);      for (j=1;j<=n;j++) 
       printf(" %.5le",matcov[i][j]);        if ((temp=fabs(a[i][j])) > big) big=temp; 
       fprintf(ficparo," %.5le",matcov[i][j]);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     }      vv[i]=1.0/big; 
     fscanf(ficpar,"\n");    } 
     printf("\n");    for (j=1;j<=n;j++) { 
     fprintf(ficparo,"\n");      for (i=1;i<j;i++) { 
   }        sum=a[i][j]; 
   for(i=1; i <=npar; i++)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     for(j=i+1;j<=npar;j++)        a[i][j]=sum; 
       matcov[i][j]=matcov[j][i];      } 
          big=0.0; 
   printf("\n");      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
         for (k=1;k<j;k++) 
     /*-------- Rewriting paramater file ----------*/          sum -= a[i][k]*a[k][j]; 
      strcpy(rfileres,"r");    /* "Rparameterfile */        a[i][j]=sum; 
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        if ( (dum=vv[i]*fabs(sum)) >= big) { 
      strcat(rfileres,".");    /* */          big=dum; 
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          imax=i; 
     if((ficres =fopen(rfileres,"w"))==NULL) {        } 
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      } 
     }      if (j != imax) { 
     fprintf(ficres,"#%s\n",version);        for (k=1;k<=n;k++) { 
              dum=a[imax][k]; 
     /*-------- data file ----------*/          a[imax][k]=a[j][k]; 
     if((fic=fopen(datafile,"r"))==NULL)    {          a[j][k]=dum; 
       printf("Problem with datafile: %s\n", datafile);goto end;        } 
     }        *d = -(*d); 
         vv[imax]=vv[j]; 
     n= lastobs;      } 
     severity = vector(1,maxwav);      indx[j]=imax; 
     outcome=imatrix(1,maxwav+1,1,n);      if (a[j][j] == 0.0) a[j][j]=TINY; 
     num=ivector(1,n);      if (j != n) { 
     moisnais=vector(1,n);        dum=1.0/(a[j][j]); 
     annais=vector(1,n);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     moisdc=vector(1,n);      } 
     andc=vector(1,n);    } 
     agedc=vector(1,n);    free_vector(vv,1,n);  /* Doesn't work */
     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);  void lubksb(double **a, int n, int *indx, double b[]) 
     anint=matrix(1,maxwav,1,n);  { 
     s=imatrix(1,maxwav+1,1,n);    int i,ii=0,ip,j; 
     adl=imatrix(1,maxwav+1,1,n);        double sum; 
     tab=ivector(1,NCOVMAX);   
     ncodemax=ivector(1,8);    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
     i=1;      sum=b[ip]; 
     while (fgets(line, MAXLINE, fic) != NULL)    {      b[ip]=b[i]; 
       if ((i >= firstobs) && (i <=lastobs)) {      if (ii) 
                for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         for (j=maxwav;j>=1;j--){      else if (sum) ii=i; 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      b[i]=sum; 
           strcpy(line,stra);    } 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    for (i=n;i>=1;i--) { 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      sum=b[i]; 
         }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
              b[i]=sum/a[i][i]; 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    } 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  } 
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  void pstamp(FILE *fichier)
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  {
     fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  }
         for (j=ncov;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  /************ Frequencies ********************/
         }  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
         num[i]=atol(stra);  {  /* Some frequencies */
            
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    int i, m, jk, j1, bool, z1,j;
           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;}*/    int first;
     double ***freq; /* Frequencies */
         i=i+1;    double *pp, **prop;
       }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     }    char fileresp[FILENAMELENGTH];
     /* printf("ii=%d", ij);    
        scanf("%d",i);*/    pp=vector(1,nlstate);
   imx=i-1; /* Number of individuals */    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
   /* for (i=1; i<=imx; i++){    strcat(fileresp,fileres);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    if((ficresp=fopen(fileresp,"w"))==NULL) {
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      printf("Problem with prevalence resultfile: %s\n", fileresp);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     }      exit(0);
     }
     for (i=1; i<=imx; i++)    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     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]));*/    j1=0;
     
   /* Calculation of the number of parameter from char model*/    j=cptcoveff;
   Tvar=ivector(1,15);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);    first=1;
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);          /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
        /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
   if (strlen(model) >1){    /*    j1++; */
     j=0, j1=0, k1=1, k2=1;    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
     j=nbocc(model,'+');        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     j1=nbocc(model,'*');          scanf("%d", i);*/
     cptcovn=j+1;        for (i=-5; i<=nlstate+ndeath; i++)  
     cptcovprod=j1;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
                for(m=iagemin; m <= iagemax+3; m++)
                  freq[i][jk][m]=0;
     strcpy(modelsav,model);        
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        for (i=1; i<=nlstate; i++)  
       printf("Error. Non available option model=%s ",model);          for(m=iagemin; m <= iagemax+3; m++)
       goto end;            prop[i][m]=0;
     }        
            dateintsum=0;
     for(i=(j+1); i>=1;i--){        k2cpt=0;
       cutv(stra,strb,modelsav,'+');        for (i=1; i<=imx; i++) {
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);          bool=1;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
       /*scanf("%d",i);*/            for (z1=1; z1<=cptcoveff; z1++)       
       if (strchr(strb,'*')) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
         cutv(strd,strc,strb,'*');                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
         if (strcmp(strc,"age")==0) {                bool=0;
           cptcovprod--;                /* 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", 
           cutv(strb,stre,strd,'V');                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
           Tvar[i]=atoi(stre);                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
           cptcovage++;                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
             Tage[cptcovage]=i;              } 
             /*printf("stre=%s ", stre);*/          }
         }   
         else if (strcmp(strd,"age")==0) {          if (bool==1){
           cptcovprod--;            for(m=firstpass; m<=lastpass; m++){
           cutv(strb,stre,strc,'V');              k2=anint[m][i]+(mint[m][i]/12.);
           Tvar[i]=atoi(stre);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
           cptcovage++;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           Tage[cptcovage]=i;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         else {                if (m<lastpass) {
           cutv(strb,stre,strc,'V');                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           Tvar[i]=ncov+k1;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
           cutv(strb,strc,strd,'V');                }
           Tprod[k1]=i;                
           Tvard[k1][1]=atoi(strc);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           Tvard[k1][2]=atoi(stre);                  dateintsum=dateintsum+k2;
           Tvar[cptcovn+k2]=Tvard[k1][1];                  k2cpt++;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                }
           for (k=1; k<=lastobs;k++)                /*}*/
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];            }
           k1++;          }
           k2=k2+2;        } /* end i */
         }         
       }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       else {        pstamp(ficresp);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        if  (cptcovn>0) {
        /*  scanf("%d",i);*/          fprintf(ficresp, "\n#********** Variable "); 
       cutv(strd,strc,strb,'V');          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       Tvar[i]=atoi(strc);          fprintf(ficresp, "**********\n#");
       }          fprintf(ficlog, "\n#********** Variable "); 
       strcpy(modelsav,stra);            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          fprintf(ficlog, "**********\n#");
         scanf("%d",i);*/        }
     }        for(i=1; i<=nlstate;i++) 
 }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
          fprintf(ficresp, "\n");
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);        
   printf("cptcovprod=%d ", cptcovprod);        for(i=iagemin; i <= iagemax+3; i++){
   scanf("%d ",i);*/          if(i==iagemax+3){
     fclose(fic);            fprintf(ficlog,"Total");
           }else{
     /*  if(mle==1){*/            if(first==1){
     if (weightopt != 1) { /* Maximisation without weights*/              first=0;
       for(i=1;i<=n;i++) weight[i]=1.0;              printf("See log file for details...\n");
     }            }
     /*-calculation of age at interview from date of interview and age at death -*/            fprintf(ficlog,"Age %d", i);
     agev=matrix(1,maxwav,1,imx);          }
           for(jk=1; jk <=nlstate ; jk++){
    for (i=1; i<=imx; i++)            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
      for(m=2; (m<= maxwav); m++)              pp[jk] += freq[jk][m][i]; 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          }
          anint[m][i]=9999;          for(jk=1; jk <=nlstate ; jk++){
          s[m][i]=-1;            for(m=-1, pos=0; m <=0 ; m++)
        }              pos += freq[jk][m][i];
                if(pp[jk]>=1.e-10){
     for (i=1; i<=imx; i++)  {              if(first==1){
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       for(m=1; (m<= maxwav); m++){              }
         if(s[m][i] >0){              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           if (s[m][i] == nlstate+1) {            }else{
             if(agedc[i]>0)              if(first==1)
               if(moisdc[i]!=99 && andc[i]!=9999)                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               agev[m][i]=agedc[i];              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             else {            }
               if (andc[i]!=9999){          }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;          for(jk=1; jk <=nlstate ; jk++){
               }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
             }              pp[jk] += freq[jk][m][i];
           }          }       
           else if(s[m][i] !=9){ /* Should no more exist */          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            pos += pp[jk];
             if(mint[m][i]==99 || anint[m][i]==9999)            posprop += prop[jk][i];
               agev[m][i]=1;          }
             else if(agev[m][i] <agemin){          for(jk=1; jk <=nlstate ; jk++){
               agemin=agev[m][i];            if(pos>=1.e-5){
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/              if(first==1)
             }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             else if(agev[m][i] >agemax){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               agemax=agev[m][i];            }else{
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/              if(first==1)
             }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             /*agev[m][i]=anint[m][i]-annais[i];*/              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             /*   agev[m][i] = age[i]+2*m;*/            }
           }            if( i <= iagemax){
           else { /* =9 */              if(pos>=1.e-5){
             agev[m][i]=1;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
             s[m][i]=-1;                /*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]);*/
         }              }
         else /*= 0 Unknown */              else
           agev[m][i]=1;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       }            }
              }
     }          
     for (i=1; i<=imx; i++)  {          for(jk=-1; jk <=nlstate+ndeath; jk++)
       for(m=1; (m<= maxwav); m++){            for(m=-1; m <=nlstate+ndeath; m++)
         if (s[m][i] > (nlstate+ndeath)) {              if(freq[jk][m][i] !=0 ) {
           printf("Error: Wrong value in nlstate or ndeath\n");                if(first==1)
           goto end;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       }              }
     }          if(i <= iagemax)
             fprintf(ficresp,"\n");
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          if(first==1)
             printf("Others in log...\n");
     free_vector(severity,1,maxwav);          fprintf(ficlog,"\n");
     free_imatrix(outcome,1,maxwav+1,1,n);        }
     free_vector(moisnais,1,n);        /*}*/
     free_vector(annais,1,n);    }
     /* free_matrix(mint,1,maxwav,1,n);    dateintmean=dateintsum/k2cpt; 
        free_matrix(anint,1,maxwav,1,n);*/   
     free_vector(moisdc,1,n);    fclose(ficresp);
     free_vector(andc,1,n);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
        free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     wav=ivector(1,imx);    /* End of Freq */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
      /************ Prevalence ********************/
     /* Concatenates waves */  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)
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
       Tcode=ivector(1,100);       We still use firstpass and lastpass as another selection.
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    */
       ncodemax[1]=1;   
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    int i, m, jk, j1, bool, z1,j;
        
    codtab=imatrix(1,100,1,10);    double **prop;
    h=0;    double posprop; 
    m=pow(2,cptcoveff);    double  y2; /* in fractional years */
      int iagemin, iagemax;
    for(k=1;k<=cptcoveff; k++){    int first; /** to stop verbosity which is redirected to log file */
      for(i=1; i <=(m/pow(2,k));i++){  
        for(j=1; j <= ncodemax[k]; j++){    iagemin= (int) agemin;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    iagemax= (int) agemax;
            h++;    /*pp=vector(1,nlstate);*/
            if (h>m) h=1;codtab[h][k]=j;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
          }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
        }    j1=0;
      }    
    }    /*j=cptcoveff;*/
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
    /*for(i=1; i <=m ;i++){    first=1;
      for(k=1; k <=cptcovn; k++){    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);      /*for(i1=1; i1<=ncodemax[k1];i1++){
      }        j1++;*/
      printf("\n");        
    }        for (i=1; i<=nlstate; i++)  
    scanf("%d",i);*/          for(m=iagemin; m <= iagemax+3; m++)
                prop[i][m]=0.0;
    /* Calculates basic frequencies. Computes observed prevalence at single age       
        and prints on file fileres'p'. */        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
              if  (cptcovn>0) {
                for (z1=1; z1<=cptcoveff; z1++) 
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                bool=0;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          } 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          if (bool==1) { 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            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 */
     /* For Powell, parameters are in a vector p[] starting at p[1]              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
     if(mle==1){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);                  /*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]]);*/
     }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                      prop[s[m][i]][iagemax+3] += weight[i]; 
     /*--------- results files --------------*/                } 
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);              }
              } /* end selection of waves */
           }
    jk=1;        }
    fprintf(ficres,"# Parameters\n");        for(i=iagemin; i <= iagemax+3; i++){  
    printf("# Parameters\n");          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
    for(i=1,jk=1; i <=nlstate; i++){            posprop += prop[jk][i]; 
      for(k=1; k <=(nlstate+ndeath); k++){          } 
        if (k != i)          
          {          for(jk=1; jk <=nlstate ; jk++){     
            printf("%d%d ",i,k);            if( i <=  iagemax){ 
            fprintf(ficres,"%1d%1d ",i,k);              if(posprop>=1.e-5){ 
            for(j=1; j <=ncovmodel; j++){                probs[i][jk][j1]= prop[jk][i]/posprop;
              printf("%f ",p[jk]);              } else{
              fprintf(ficres,"%f ",p[jk]);                if(first==1){
              jk++;                  first=0;
            }                  printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
            printf("\n");                }
            fprintf(ficres,"\n");              }
          }            } 
      }          }/* end jk */ 
    }        }/* end i */ 
  if(mle==1){      /*} *//* end i1 */
     /* Computing hessian and covariance matrix */    } /* end j1 */
     ftolhess=ftol; /* Usually correct */    
     hesscov(matcov, p, npar, delti, ftolhess, func);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
  }    /*free_vector(pp,1,nlstate);*/
     fprintf(ficres,"# Scales\n");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     printf("# Scales\n");  }  /* End of prevalence */
      for(i=1,jk=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){  /************* Waves Concatenation ***************/
         if (j!=i) {  
           fprintf(ficres,"%1d%1d",i,j);  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
           printf("%1d%1d",i,j);  {
           for(k=1; k<=ncovmodel;k++){    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
             printf(" %.5e",delti[jk]);       Death is a valid wave (if date is known).
             fprintf(ficres," %.5e",delti[jk]);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
             jk++;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           }       and mw[mi+1][i]. dh depends on stepm.
           printf("\n");       */
           fprintf(ficres,"\n");  
         }    int i, mi, m;
       }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
      }       double sum=0., jmean=0.;*/
        int first;
     k=1;    int j, k=0,jk, ju, jl;
     fprintf(ficres,"# Covariance\n");    double sum=0.;
     printf("# Covariance\n");    first=0;
     for(i=1;i<=npar;i++){    jmin=100000;
       /*  if (k>nlstate) k=1;    jmax=-1;
       i1=(i-1)/(ncovmodel*nlstate)+1;    jmean=0.;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    for(i=1; i<=imx; i++){
       printf("%s%d%d",alph[k],i1,tab[i]);*/      mi=0;
       fprintf(ficres,"%3d",i);      m=firstpass;
       printf("%3d",i);      while(s[m][i] <= nlstate){
       for(j=1; j<=i;j++){        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
         fprintf(ficres," %.5e",matcov[i][j]);          mw[++mi][i]=m;
         printf(" %.5e",matcov[i][j]);        if(m >=lastpass)
       }          break;
       fprintf(ficres,"\n");        else
       printf("\n");          m++;
       k++;      }/* end while */
     }      if (s[m][i] > nlstate){
            mi++;     /* Death is another wave */
     while((c=getc(ficpar))=='#' && c!= EOF){        /* if(mi==0)  never been interviewed correctly before death */
       ungetc(c,ficpar);           /* Only death is a correct wave */
       fgets(line, MAXLINE, ficpar);        mw[mi][i]=m;
       puts(line);      }
       fputs(line,ficparo);  
     }      wav[i]=mi;
     ungetc(c,ficpar);      if(mi==0){
          nbwarn++;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);        if(first==0){
              printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     if (fage <= 2) {          first=1;
       bage = agemin;        }
       fage = agemaxpar;        if(first==1){
     }          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
            }
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      } /* end mi==0 */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);    } /* End individuals */
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);  
      for(i=1; i<=imx; i++){
     while((c=getc(ficpar))=='#' && c!= EOF){      for(mi=1; mi<wav[i];mi++){
     ungetc(c,ficpar);        if (stepm <=0)
     fgets(line, MAXLINE, ficpar);          dh[mi][i]=1;
     puts(line);        else{
     fputs(line,ficparo);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   }            if (agedc[i] < 2*AGESUP) {
   ungetc(c,ficpar);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                if(j==0) j=1;  /* Survives at least one month after exam */
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);              else if(j<0){
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                nberr++;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                      j=1; /* Temporary Dangerous patch */
   while((c=getc(ficpar))=='#' && c!= EOF){                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);
     ungetc(c,ficpar);                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]);
     fgets(line, MAXLINE, ficpar);                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);
     puts(line);              }
     fputs(line,ficparo);              k=k+1;
   }              if (j >= jmax){
   ungetc(c,ficpar);                jmax=j;
                  ijmax=i;
               }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;              if (j <= jmin){
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                jmin=j;
                 ijmin=i;
   fscanf(ficpar,"pop_based=%d\n",&popbased);              }
   fprintf(ficparo,"pop_based=%d\n",popbased);                sum=sum+j;
   fprintf(ficres,"pop_based=%d\n",popbased);                /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          else{
     puts(line);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     fputs(line,ficparo);  /*        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]); */
   }  
   ungetc(c,ficpar);            k=k+1;
             if (j >= jmax) {
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);              jmax=j;
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);              ijmax=i;
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);            }
             else if (j <= jmin){
               jmin=j;
 while((c=getc(ficpar))=='#' && c!= EOF){              ijmin=i;
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     puts(line);            /*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]);*/
     fputs(line,ficparo);            if(j<0){
   }              nberr++;
   ungetc(c,ficpar);              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]);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);            }
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            sum=sum+j;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          }
           jk= j/stepm;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
 /*------------ gnuplot -------------*/          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);            if(jl==0){
                dh[mi][i]=jk;
 /*------------ free_vector  -------------*/              bh[mi][i]=0;
  chdir(path);            }else{ /* We want a negative bias in order to only have interpolation ie
                      * to avoid the price of an extra matrix product in likelihood */
  free_ivector(wav,1,imx);              dh[mi][i]=jk+1;
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);              bh[mi][i]=ju;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);              }
  free_ivector(num,1,n);          }else{
  free_vector(agedc,1,n);            if(jl <= -ju){
  /*free_matrix(covar,1,NCOVMAX,1,n);*/              dh[mi][i]=jk;
  fclose(ficparo);              bh[mi][i]=jl;       /* bias is positive if real duration
  fclose(ficres);                                   * is higher than the multiple of stepm and negative otherwise.
                                    */
 /*--------- index.htm --------*/            }
             else{
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
              }
   /*--------------- Prevalence limit --------------*/            if(dh[mi][i]==0){
                dh[mi][i]=1; /* At least one step */
   strcpy(filerespl,"pl");              bh[mi][i]=ju; /* At least one step */
   strcat(filerespl,fileres);              /*  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);*/
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          } /* end if mle */
   }        }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      } /* end wave */
   fprintf(ficrespl,"#Prevalence limit\n");    }
   fprintf(ficrespl,"#Age ");    jmean=sum/k;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    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(ficrespl,"\n");    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
     }
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /*********** Tricode ****************************/
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  {
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   k=0;     * Boring subroutine which should only output nbcode[Tvar[j]][k]
   agebase=agemin;     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
   agelim=agemaxpar;     * nbcode[Tvar[j]][1]= 
   ftolpl=1.e-10;    */
   i1=cptcoveff;  
   if (cptcovn < 1){i1=1;}    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     int modmaxcovj=0; /* Modality max of covariates j */
   for(cptcov=1;cptcov<=i1;cptcov++){    int cptcode=0; /* Modality max of covariates j */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int modmincovj=0; /* Modality min of covariates j */
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");    cptcoveff=0; 
         for(j=1;j<=cptcoveff;j++)   
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for (k=-1; k < maxncov; k++) Ndum[k]=0;
         fprintf(ficrespl,"******\n");    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
          
         for (age=agebase; age<=agelim; age++){    /* Loop on covariates without age and products */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
           fprintf(ficrespl,"%.0f",age );      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
           for(i=1; i<=nlstate;i++)                                 modality of this covariate Vj*/ 
           fprintf(ficrespl," %.5f", prlim[i][i]);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
           fprintf(ficrespl,"\n");                                      * If product of Vn*Vm, still boolean *:
         }                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
       }                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
     }        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
   fclose(ficrespl);                                        modality of the nth covariate of individual i. */
         if (ij > modmaxcovj)
   /*------------- h Pij x at various ages ------------*/          modmaxcovj=ij; 
          else if (ij < modmincovj) 
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          modmincovj=ij; 
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        if ((ij < -1) && (ij > NCOVMAX)){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   }          exit(1);
   printf("Computing pij: result on file '%s' \n", filerespij);        }else
          Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   /*if (stepm<=24) stepsize=2;*/        /*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
   agelim=AGESUP;           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
   hstepm=stepsize*YEARM; /* Every year of age */           female is 1, then modmaxcovj=1.*/
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      }
        printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   k=0;      cptcode=modmaxcovj;
   for(cptcov=1;cptcov<=i1;cptcov++){      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     /*for (i=0; i<=cptcode; i++) {*/
       k=k+1;      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
         fprintf(ficrespij,"\n#****** ");        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
         for(j=1;j<=cptcoveff;j++)        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
         fprintf(ficrespij,"******\n");        }
                /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      } /* Ndum[-1] number of undefined modalities */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
           oldm=oldms;savm=savms;      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
           fprintf(ficrespij,"# Age");         modmincovj=3; modmaxcovj = 7;
           for(i=1; i<=nlstate;i++)         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
             for(j=1; j<=nlstate+ndeath;j++)         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
               fprintf(ficrespij," %1d-%1d",i,j);         variables V1_1 and V1_2.
           fprintf(ficrespij,"\n");         nbcode[Tvar[j]][ij]=k;
           for (h=0; h<=nhstepm; h++){         nbcode[Tvar[j]][1]=0;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );         nbcode[Tvar[j]][2]=1;
             for(i=1; i<=nlstate;i++)         nbcode[Tvar[j]][3]=2;
               for(j=1; j<=nlstate+ndeath;j++)      */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      ij=1; /* ij is similar to i but can jumps over null modalities */
             fprintf(ficrespij,"\n");      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 */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          /*recode from 0 */
           fprintf(ficrespij,"\n");          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
         }            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
     }                                       k is a modality. If we have model=V1+V1*sex 
   }                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
             ij++;
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/          }
           if (ij > ncodemax[j]) break; 
   fclose(ficrespij);        }  /* end of loop on */
       } /* end of loop on modality */ 
     } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   /*---------- Forecasting ------------------*/    
   if(stepm == 1) {   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
     free_matrix(mint,1,maxwav,1,n);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
     free_vector(weight,1,n);}     Ndum[ij]++; 
   else{   } 
     erreur=108;  
     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);   ij=1;
   }   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
       /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
      if((Ndum[i]!=0) && (i<=ncovcol)){
   /*---------- Health expectancies and variances ------------*/       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
        Tvaraff[ij]=i; /*For printing (unclear) */
   strcpy(filerest,"t");       ij++;
   strcat(filerest,fileres);     }else
   if((ficrest=fopen(filerest,"w"))==NULL) {         Tvaraff[ij]=0;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;   }
   }   ij--;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);   cptcoveff=ij; /*Number of total covariates*/
   
   }
   strcpy(filerese,"e");  
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {  /*********** Health Expectancies ****************/
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
   {
  strcpy(fileresv,"v");    /* Health expectancies, no variances */
   strcat(fileresv,fileres);    int i, j, nhstepm, hstepm, h, nstepm;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    int nhstepma, nstepma; /* Decreasing with age */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    double age, agelim, hf;
   }    double ***p3mat;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    double eip;
   
   k=0;    pstamp(ficreseij);
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficreseij,"# Age");
       k=k+1;    for(i=1; i<=nlstate;i++){
       fprintf(ficrest,"\n#****** ");      for(j=1; j<=nlstate;j++){
       for(j=1;j<=cptcoveff;j++)        fprintf(ficreseij," e%1d%1d ",i,j);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      }
       fprintf(ficrest,"******\n");      fprintf(ficreseij," e%1d. ",i);
     }
       fprintf(ficreseij,"\n#****** ");    fprintf(ficreseij,"\n");
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    
       fprintf(ficreseij,"******\n");    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
       fprintf(ficresvij,"\n#****** ");    }
       for(j=1;j<=cptcoveff;j++)    else  hstepm=estepm;   
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    /* We compute the life expectancy from trapezoids spaced every estepm months
       fprintf(ficresvij,"******\n");     * 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
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     * we are calculating an estimate of the Life Expectancy assuming a linear 
       oldm=oldms;savm=savms;     * progression in between and thus overestimating or underestimating according
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);       * to the curvature of the survival function. If, for the same date, we 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       oldm=oldms;savm=savms;     * to compare the new estimate of Life expectancy with the same linear 
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);     * 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 */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);       nhstepm is the number of hstepm from age to agelim 
       fprintf(ficrest,"\n");       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
       hf=1;       and note for a fixed period like estepm months */
       if (stepm >= YEARM) hf=stepm/YEARM;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       epj=vector(1,nlstate+1);       survival function given by stepm (the optimization length). Unfortunately it
       for(age=bage; age <=fage ;age++){       means that if the survival funtion is printed only each two years of age and if
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         if (popbased==1) {       results. So we changed our mind and took the option of the best precision.
           for(i=1; i<=nlstate;i++)    */
             prlim[i][i]=probs[(int)age][i][k];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         }  
            agelim=AGESUP;
         fprintf(ficrest," %.0f",age);    /* If stepm=6 months */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           for(i=1, epj[j]=0.;i <=nlstate;i++) {         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];      
           }  /* nhstepm age range expressed in number of stepm */
           epj[nlstate+1] +=epj[j];    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         for(i=1, vepp=0.;i <=nlstate;i++)    /* if (stepm >= YEARM) hstepm=1;*/
           for(j=1;j <=nlstate;j++)    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
             vepp += vareij[i][j][(int)age];    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));  
         for(j=1;j <=nlstate;j++){    for (age=bage; age<=fage; age ++){ 
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         fprintf(ficrest,"\n");      /* 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
   fclose(ficreseij);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   fclose(ficresvij);      
   fclose(ficrest);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   fclose(ficpar);      
   free_vector(epj,1,nlstate+1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        
   /*------- Variance limit prevalence------*/        printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   strcpy(fileresvpl,"vpl");      
   strcat(fileresvpl,fileres);      /* Computing expectancies */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      for(i=1; i<=nlstate;i++)
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        for(j=1; j<=nlstate;j++)
     exit(0);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   }            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);            
             /* 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]);*/
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){          }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;      fprintf(ficreseij,"%3.0f",age );
       fprintf(ficresvpl,"\n#****** ");      for(i=1; i<=nlstate;i++){
       for(j=1;j<=cptcoveff;j++)        eip=0;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1; j<=nlstate;j++){
       fprintf(ficresvpl,"******\n");          eip +=eij[i][j][(int)age];
                fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
       varpl=matrix(1,nlstate,(int) bage, (int) fage);        }
       oldm=oldms;savm=savms;        fprintf(ficreseij,"%9.4f", eip );
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      }
     }      fprintf(ficreseij,"\n");
  }      
     }
   fclose(ficresvpl);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
   /*---------- End : free ----------------*/    fprintf(ficlog,"\n");
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    
    }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  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[] )
    
    {
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    /* Covariances of health expectancies eij and of total life expectancies according
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);     to initial status i, ei. .
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
      int nhstepma, nstepma; /* Decreasing with age */
   free_matrix(matcov,1,npar,1,npar);    double age, agelim, hf;
   free_vector(delti,1,npar);    double ***p3matp, ***p3matm, ***varhe;
   free_matrix(agev,1,maxwav,1,imx);    double **dnewm,**doldm;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    double *xp, *xm;
     double **gp, **gm;
   if(erreur >0)    double ***gradg, ***trgradg;
     printf("End of Imach with error %d\n",erreur);    int theta;
   else   printf("End of Imach\n");  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    double eip, vip;
    
   /* 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);*/    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    xp=vector(1,npar);
   /*------ End -----------*/    xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
  end:    
 #ifdef windows    pstamp(ficresstdeij);
   /* chdir(pathcd);*/    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
 #endif    fprintf(ficresstdeij,"# Age");
  /*system("wgnuplot graph.plt");*/    for(i=1; i<=nlstate;i++){
  /*system("../gp37mgw/wgnuplot graph.plt");*/      for(j=1; j<=nlstate;j++)
  /*system("cd ../gp37mgw");*/        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      fprintf(ficresstdeij," e%1d. ",i);
  strcpy(plotcmd,GNUPLOTPROGRAM);    }
  strcat(plotcmd," ");    fprintf(ficresstdeij,"\n");
  strcat(plotcmd,optionfilegnuplot);  
  system(plotcmd);    pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
 #ifdef windows    fprintf(ficrescveij,"# Age");
   while (z[0] != 'q') {    for(i=1; i<=nlstate;i++)
     chdir(path);      for(j=1; j<=nlstate;j++){
     printf("\nType e to edit output files, c to start again, and q for exiting: ");        cptj= (j-1)*nlstate+i;
     scanf("%s",z);        for(i2=1; i2<=nlstate;i2++)
     if (z[0] == 'c') system("./imach");          for(j2=1; j2<=nlstate;j2++){
     else if (z[0] == 'e') {            cptj2= (j2-1)*nlstate+i2;
       chdir(path);            if(cptj2 <= cptj)
       system(optionfilehtm);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     }          }
     else if (z[0] == 'q') exit(0);      }
   }    fprintf(ficrescveij,"\n");
 #endif    
 }    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     /* 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"*/
      /* command line Intel compiler 32bit windows, XP compatible:*/
      /* /GS /W3 /Gy
         /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
         "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
         "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
         /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch" 
         /* 64 bits */
      /*
        /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
        /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
        /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
        "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
      /* Optimization are useless and O3 is slower than O2 */
      /*
        /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
        /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
        /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
        /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 
      */
      /* Link is $/ /* /OUT:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
         /PDB:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
         "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
         "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
         "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
         /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
         /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
         uiAccess='false'"
         /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
         /NOLOGO /TLBID:1
      */
   #if defined __INTEL_COMPILER
   #if defined(__GNUC__)
           struct utsname sysInfo;  /* For Intel on Linux and OS/X */
   #endif
   #elif defined(__GNUC__) 
   #ifndef  __APPLE__
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
      struct utsname sysInfo;
      int cross = CROSS;
      if (cross){
              printf("Cross-");
              fprintf(ficlog, "Cross-");
      }
   #endif
   
   #include <stdint.h>
   
      printf("Compiled with:");fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for ");fprintf(ficlog," for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     double ftolpl = 1.e-10;
     double age, agebase, agelim;
   
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
       agebase=ageminpar;
       agelim=agemaxpar;
   
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           fprintf(ficrespl,"#Age ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
           fprintf(ficrespl,"\n");
           
           for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
           return 0;
   }
   
   int hPijx(double *p, int bage, int fage){
       /*------------- h Pij x at various ages ------------*/
   
     int stepsize;
     int agelim;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
   
     double agedeb;
     double ***p3mat;
   
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       i1= pow(2,cptcoveff);
      /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
      /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
      /*   k=k+1;  */
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
         
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
           
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
             fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
         /*}*/
       }
           return 0;
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
   #ifdef WIN32
     _getcwd(pathcd, size);
   #else
     getcwd(pathcd, size);
   #endif
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   #ifdef WIN32
     _chdir(path); /* Can be a relative path */
     if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
   #else
     chdir(path); /* Can be a relative path */
     if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
   #endif
     printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* 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);
   #ifdef WIN32
     _chdir(optionfilefiname); /* Move to directory named optionfile */
   #else
     chdir(optionfilefiname); /* Move to directory named optionfile */
   #endif
             
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
       /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar);
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
   #ifdef WIN32
      if (_chdir(pathcd) != 0)
              printf("Can't move to directory %s!\n",path);
      if(_getcwd(pathcd,MAXLINE) > 0)
   #else
      if(chdir(pathcd) != 0)
              printf("Can't move to directory %s!\n", path);
      if (getcwd(pathcd, MAXLINE) > 0)
   #endif 
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.29  
changed lines
  Added in v.1.185


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