Diff for /imach/src/imach.c between versions 1.37 and 1.173

version 1.37, 2002/03/29 15:31:59 version 1.173, 2015/01/03 12:06:26
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.173  2015/01/03 12:06:26  brouard
      Summary: trying to detect cross-compilation
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.172  2014/12/27 12:07:47  brouard
   first survey ("cross") where individuals from different ages are    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   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 1.171  2014/12/23 13:26:59  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: Back from Visual C
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Still problem with utsname.h on Windows
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.170  2014/12/23 11:17:12  brouard
   simplest model is the multinomial logistic model where pij is the    Summary: Cleaning some \%% back to %%
   probabibility to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    The escape was mandatory for a specific compiler (which one?), but too many warnings.
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.169  2014/12/22 23:08:31  brouard
   complex model than "constant and age", you should modify the program    Summary: 0.98p
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Outputs some informations on compiler used, OS etc. Testing on different platforms.
   convergence.  
     Revision 1.168  2014/12/22 15:17:42  brouard
   The advantage of this computer programme, compared to a simple    Summary: update
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.167  2014/12/22 13:50:56  brouard
   intermediate interview, the information is lost, but taken into    Summary: Testing uname and compiler version and if compiled 32 or 64
   account using an interpolation or extrapolation.    
     Testing on Linux 64
   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 1.166  2014/12/22 11:40:47  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 1.165  2014/12/16 11:20:36  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    Summary: After compiling on Visual C
   and the contribution of each individual to the likelihood is simply  
   hPijx.    * imach.c (Module): Merging 1.61 to 1.162
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.164  2014/12/16 10:52:11  brouard
   of the life expectancies. It also computes the prevalence limits.    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    * imach.c (Module): Merging 1.61 to 1.162
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.163  2014/12/16 10:30:11  brouard
   from the European Union.    * imach.c (Module): Merging 1.61 to 1.162
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.162  2014/09/25 11:43:39  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Summary: temporary backup 0.99!
   **********************************************************************/  
      Revision 1.1  2014/09/16 11:06:58  brouard
 #include <math.h>    Summary: With some code (wrong) for nlopt
 #include <stdio.h>  
 #include <stdlib.h>    Author:
 #include <unistd.h>  
     Revision 1.161  2014/09/15 20:41:41  brouard
 #define MAXLINE 256    Summary: Problem with macro SQR on Intel compiler
 #define GNUPLOTPROGRAM "wgnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.160  2014/09/02 09:24:05  brouard
 #define FILENAMELENGTH 80    *** empty log message ***
 /*#define DEBUG*/  
 #define windows    Revision 1.159  2014/09/01 10:34:10  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Summary: WIN32
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Author: Brouard
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.158  2014/08/27 17:11:51  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    *** empty log message ***
   
 #define NINTERVMAX 8    Revision 1.157  2014/08/27 16:26:55  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Summary: Preparing windows Visual studio version
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Author: Brouard
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    In order to compile on Visual studio, time.h is now correct and time_t
 #define YEARM 12. /* Number of months per year */    and tm struct should be used. difftime should be used but sometimes I
 #define AGESUP 130    just make the differences in raw time format (time(&now).
 #define AGEBASE 40    Trying to suppress #ifdef LINUX
     Add xdg-open for __linux in order to open default browser.
   
 int erreur; /* Error number */    Revision 1.156  2014/08/25 20:10:10  brouard
 int nvar;    *** empty log message ***
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.155  2014/08/25 18:32:34  brouard
 int nlstate=2; /* Number of live states */    Summary: New compile, minor changes
 int ndeath=1; /* Number of dead states */    Author: Brouard
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.154  2014/06/20 17:32:08  brouard
     Summary: Outputs now all graphs of convergence to period prevalence
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.153  2014/06/20 16:45:46  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    Summary: If 3 live state, convergence to period prevalence on same graph
 int mle, weightopt;    Author: Brouard
 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 1.152  2014/06/18 17:54:09  brouard
 double jmean; /* Mean space between 2 waves */    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.151  2014/06/18 16:43:30  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    *** empty log message ***
 FILE *ficgp,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.150  2014/06/18 16:42:35  brouard
   char filerese[FILENAMELENGTH];    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
  FILE  *ficresvij;    Author: brouard
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.149  2014/06/18 15:51:14  brouard
   char fileresvpl[FILENAMELENGTH];    Summary: Some fixes in parameter files errors
     Author: Nicolas Brouard
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.148  2014/06/17 17:38:48  brouard
 #define FTOL 1.0e-10    Summary: Nothing new
     Author: Brouard
 #define NRANSI  
 #define ITMAX 200    Just a new packaging for OS/X version 0.98nS
   
 #define TOL 2.0e-4    Revision 1.147  2014/06/16 10:33:11  brouard
     *** empty log message ***
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.146  2014/06/16 10:20:28  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Summary: Merge
     Author: Brouard
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Merge, before building revised version.
 #define TINY 1.0e-20  
     Revision 1.145  2014/06/10 21:23:15  brouard
 static double maxarg1,maxarg2;    Summary: Debugging with valgrind
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Author: Nicolas Brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Lot of changes in order to output the results with some covariates
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    After the Edimburgh REVES conference 2014, it seems mandatory to
 #define rint(a) floor(a+0.5)    improve the code.
     No more memory valgrind error but a lot has to be done in order to
 static double sqrarg;    continue the work of splitting the code into subroutines.
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Also, decodemodel has been improved. Tricode is still not
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    optimal. nbcode should be improved. Documentation has been added in
     the source code.
 int imx;  
 int stepm;    Revision 1.143  2014/01/26 09:45:38  brouard
 /* Stepm, step in month: minimum step interpolation*/    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   
 int estepm;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   
 int m,nb;    Revision 1.142  2014/01/26 03:57:36  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 double dateintmean=0;  
     Revision 1.141  2014/01/26 02:42:01  brouard
 double *weight;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.140  2011/09/02 10:37:54  brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Summary: times.h is ok with mingw32 now.
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.139  2010/06/14 07:50:17  brouard
 double ftolhess; /* Tolerance for computing hessian */    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
     I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.138  2010/04/30 18:19:40  brouard
 {    *** empty log message ***
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.137  2010/04/29 18:11:38  brouard
     (Module): Checking covariates for more complex models
    l1 = strlen( path );                 /* length of path */    than V1+V2. A lot of change to be done. Unstable.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    Revision 1.136  2010/04/26 20:30:53  brouard
    s = strrchr( path, '\\' );           /* find last / */    (Module): merging some libgsl code. Fixing computation
 #else    of likelione (using inter/intrapolation if mle = 0) in order to
    s = strrchr( path, '/' );            /* find last / */    get same likelihood as if mle=1.
 #endif    Some cleaning of code and comments added.
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.135  2009/10/29 15:33:14  brouard
       extern char       *getwd( );    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.134  2009/10/29 13:18:53  brouard
 #else    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
       extern char       *getcwd( );  
     Revision 1.133  2009/07/06 10:21:25  brouard
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    just nforces
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.132  2009/07/06 08:22:05  brouard
       }    Many tings
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.131  2009/06/20 16:22:47  brouard
       s++;                              /* after this, the filename */    Some dimensions resccaled
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.130  2009/05/26 06:44:34  brouard
       strcpy( name, s );                /* save file name */    (Module): Max Covariate is now set to 20 instead of 8. A
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    lot of cleaning with variables initialized to 0. Trying to make
       dirc[l1-l2] = 0;                  /* add zero */    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
    }  
    l1 = strlen( dirc );                 /* length of directory */    Revision 1.129  2007/08/31 13:49:27  lievre
 #ifdef windows    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Revision 1.128  2006/06/30 13:02:05  brouard
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    (Module): Clarifications on computing e.j
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.127  2006/04/28 18:11:50  brouard
    s++;    (Module): Yes the sum of survivors was wrong since
    strcpy(ext,s);                       /* save extension */    imach-114 because nhstepm was no more computed in the age
    l1= strlen( name);    loop. Now we define nhstepma in the age loop.
    l2= strlen( s)+1;    (Module): In order to speed up (in case of numerous covariates) we
    strncpy( finame, name, l1-l2);    compute health expectancies (without variances) in a first step
    finame[l1-l2]= 0;    and then all the health expectancies with variances or standard
    return( 0 );                         /* we're done */    deviation (needs data from the Hessian matrices) which slows the
 }    computation.
     In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
 /******************************************/  
     Revision 1.126  2006/04/28 17:23:28  brouard
 void replace(char *s, char*t)    (Module): Yes the sum of survivors was wrong since
 {    imach-114 because nhstepm was no more computed in the age
   int i;    loop. Now we define nhstepma in the age loop.
   int lg=20;    Version 0.98h
   i=0;  
   lg=strlen(t);    Revision 1.125  2006/04/04 15:20:31  lievre
   for(i=0; i<= lg; i++) {    Errors in calculation of health expectancies. Age was not initialized.
     (s[i] = t[i]);    Forecasting file added.
     if (t[i]== '\\') s[i]='/';  
   }    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
 int nbocc(char *s, char occ)  
 {    Revision 1.123  2006/03/20 10:52:43  brouard
   int i,j=0;    * imach.c (Module): <title> changed, corresponds to .htm file
   int lg=20;    name. <head> headers where missing.
   i=0;  
   lg=strlen(s);    * imach.c (Module): Weights can have a decimal point as for
   for(i=0; i<= lg; i++) {    English (a comma might work with a correct LC_NUMERIC environment,
   if  (s[i] == occ ) j++;    otherwise the weight is truncated).
   }    Modification of warning when the covariates values are not 0 or
   return j;    1.
 }    Version 0.98g
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.122  2006/03/20 09:45:41  brouard
 {    (Module): Weights can have a decimal point as for
   int i,lg,j,p=0;    English (a comma might work with a correct LC_NUMERIC environment,
   i=0;    otherwise the weight is truncated).
   for(j=0; j<=strlen(t)-1; j++) {    Modification of warning when the covariates values are not 0 or
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    1.
   }    Version 0.98g
   
   lg=strlen(t);    Revision 1.121  2006/03/16 17:45:01  lievre
   for(j=0; j<p; j++) {    * imach.c (Module): Comments concerning covariates added
     (u[j] = t[j]);  
   }    * imach.c (Module): refinements in the computation of lli if
      u[p]='\0';    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Revision 1.120  2006/03/16 15:10:38  lievre
   }    (Module): refinements in the computation of lli if
 }    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 /********************** nrerror ********************/  
     Revision 1.119  2006/03/15 17:42:26  brouard
 void nrerror(char error_text[])    (Module): Bug if status = -2, the loglikelihood was
 {    computed as likelihood omitting the logarithm. Version O.98e
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.118  2006/03/14 18:20:07  brouard
   exit(1);    (Module): varevsij Comments added explaining the second
 }    table of variances if popbased=1 .
 /*********************** vector *******************/    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 double *vector(int nl, int nh)    (Module): Function pstamp added
 {    (Module): Version 0.98d
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.117  2006/03/14 17:16:22  brouard
   if (!v) nrerror("allocation failure in vector");    (Module): varevsij Comments added explaining the second
   return v-nl+NR_END;    table of variances if popbased=1 .
 }    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 /************************ free vector ******************/    (Module): Version 0.98d
 void free_vector(double*v, int nl, int nh)  
 {    Revision 1.116  2006/03/06 10:29:27  brouard
   free((FREE_ARG)(v+nl-NR_END));    (Module): Variance-covariance wrong links and
 }    varian-covariance of ej. is needed (Saito).
   
 /************************ivector *******************************/    Revision 1.115  2006/02/27 12:17:45  brouard
 int *ivector(long nl,long nh)    (Module): One freematrix added in mlikeli! 0.98c
 {  
   int *v;    Revision 1.114  2006/02/26 12:57:58  brouard
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    (Module): Some improvements in processing parameter
   if (!v) nrerror("allocation failure in ivector");    filename with strsep.
   return v-nl+NR_END;  
 }    Revision 1.113  2006/02/24 14:20:24  brouard
     (Module): Memory leaks checks with valgrind and:
 /******************free ivector **************************/    datafile was not closed, some imatrix were not freed and on matrix
 void free_ivector(int *v, long nl, long nh)    allocation too.
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.112  2006/01/30 09:55:26  brouard
 }    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
 /******************* imatrix *******************************/    Revision 1.111  2006/01/25 20:38:18  brouard
 int **imatrix(long nrl, long nrh, long ncl, long nch)    (Module): Lots of cleaning and bugs added (Gompertz)
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    (Module): Comments can be added in data file. Missing date values
 {    can be a simple dot '.'.
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    Revision 1.110  2006/01/25 00:51:50  brouard
      (Module): Lots of cleaning and bugs added (Gompertz)
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Revision 1.109  2006/01/24 19:37:15  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Comments (lines starting with a #) are allowed in data.
   m += NR_END;  
   m -= nrl;    Revision 1.108  2006/01/19 18:05:42  lievre
      Gnuplot problem appeared...
      To be fixed
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Revision 1.107  2006/01/19 16:20:37  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Test existence of gnuplot in imach path
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.106  2006/01/19 13:24:36  brouard
      Some cleaning and links added in html output
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
      Revision 1.105  2006/01/05 20:23:19  lievre
   /* return pointer to array of pointers to rows */    *** empty log message ***
   return m;  
 }    Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 /****************** free_imatrix *************************/    (Module): If the status is missing at the last wave but we know
 void free_imatrix(m,nrl,nrh,ncl,nch)    that the person is alive, then we can code his/her status as -2
       int **m;    (instead of missing=-1 in earlier versions) and his/her
       long nch,ncl,nrh,nrl;    contributions to the likelihood is 1 - Prob of dying from last
      /* free an int matrix allocated by imatrix() */    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 {    the healthy state at last known wave). Version is 0.98
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Revision 1.103  2005/09/30 15:54:49  lievre
 }    (Module): sump fixed, loop imx fixed, and simplifications.
   
 /******************* matrix *******************************/    Revision 1.102  2004/09/15 17:31:30  brouard
 double **matrix(long nrl, long nrh, long ncl, long nch)    Add the possibility to read data file including tab characters.
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    Revision 1.101  2004/09/15 10:38:38  brouard
   double **m;    Fix on curr_time
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.100  2004/07/12 18:29:06  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    Add version for Mac OS X. Just define UNIX in Makefile
   m += NR_END;  
   m -= nrl;    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.98  2004/05/16 15:05:56  brouard
   m[nrl] += NR_END;    New version 0.97 . First attempt to estimate force of mortality
   m[nrl] -= ncl;    directly from the data i.e. without the need of knowing the health
     state at each age, but using a Gompertz model: log u =a + b*age .
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    This is the basic analysis of mortality and should be done before any
   return m;    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.
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    The same imach parameter file can be used but the option for mle should be -3.
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Agnès, who wrote this part of the code, tried to keep most of the
   free((FREE_ARG)(m+nrl-NR_END));    former routines in order to include the new code within the former code.
 }  
     The output is very simple: only an estimate of the intercept and of
 /******************* ma3x *******************************/    the slope with 95% confident intervals.
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {    Current limitations:
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    A) Even if you enter covariates, i.e. with the
   double ***m;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     B) There is no computation of Life Expectancy nor Life Table.
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.97  2004/02/20 13:25:42  lievre
   m += NR_END;    Version 0.96d. Population forecasting command line is (temporarily)
   m -= nrl;    suppressed.
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Revision 1.96  2003/07/15 15:38:55  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   m[nrl] += NR_END;    rewritten within the same printf. Workaround: many printfs.
   m[nrl] -= ncl;  
     Revision 1.95  2003/07/08 07:54:34  brouard
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    matrix (cov(a12,c31) instead of numbers.
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;    Revision 1.94  2003/06/27 13:00:02  brouard
   m[nrl][ncl] -= nll;    Just cleaning
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;    Revision 1.93  2003/06/25 16:33:55  brouard
      (Module): On windows (cygwin) function asctime_r doesn't
   for (i=nrl+1; i<=nrh; i++) {    exist so I changed back to asctime which exists.
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    (Module): Version 0.96b
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;    Revision 1.92  2003/06/25 16:30:45  brouard
   }    (Module): On windows (cygwin) function asctime_r doesn't
   return m;    exist so I changed back to asctime which exists.
 }  
     Revision 1.91  2003/06/25 15:30:29  brouard
 /*************************free ma3x ************************/    * imach.c (Repository): Duplicated warning errors corrected.
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    (Repository): Elapsed time after each iteration is now output. It
 {    helps to forecast when convergence will be reached. Elapsed time
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    is stamped in powell.  We created a new html file for the graphs
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    concerning matrix of covariance. It has extension -cov.htm.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 /***************** f1dim *************************/    mle=-1 a template is output in file "or"mypar.txt with the design
 extern int ncom;    of the covariance matrix to be input.
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);    Revision 1.89  2003/06/24 12:30:52  brouard
      (Module): Some bugs corrected for windows. Also, when
 double f1dim(double x)    mle=-1 a template is output in file "or"mypar.txt with the design
 {    of the covariance matrix to be input.
   int j;  
   double f;    Revision 1.88  2003/06/23 17:54:56  brouard
   double *xt;    * 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.
    
   xt=vector(1,ncom);    Revision 1.87  2003/06/18 12:26:01  brouard
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    Version 0.96
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);    Revision 1.86  2003/06/17 20:04:08  brouard
   return f;    (Module): Change position of html and gnuplot routines and added
 }    routine fileappend.
   
 /*****************brent *************************/    Revision 1.85  2003/06/17 13:12:43  brouard
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    * imach.c (Repository): Check when date of death was earlier that
 {    current date of interview. It may happen when the death was just
   int iter;    prior to the death. In this case, dh was negative and likelihood
   double a,b,d,etemp;    was wrong (infinity). We still send an "Error" but patch by
   double fu,fv,fw,fx;    assuming that the date of death was just one stepm after the
   double ftemp;    interview.
   double p,q,r,tol1,tol2,u,v,w,x,xm;    (Repository): Because some people have very long ID (first column)
   double e=0.0;    we changed int to long in num[] and we added a new lvector for
      memory allocation. But we also truncated to 8 characters (left
   a=(ax < cx ? ax : cx);    truncation)
   b=(ax > cx ? ax : cx);    (Repository): No more line truncation errors.
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);    Revision 1.84  2003/06/13 21:44:43  brouard
   for (iter=1;iter<=ITMAX;iter++) {    * imach.c (Repository): Replace "freqsummary" at a correct
     xm=0.5*(a+b);    place. It differs from routine "prevalence" which may be called
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    many times. Probs is memory consuming and must be used with
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    parcimony.
     printf(".");fflush(stdout);    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #ifdef DEBUG  
     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);    Revision 1.83  2003/06/10 13:39:11  lievre
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    *** empty log message ***
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    Revision 1.82  2003/06/05 15:57:20  brouard
       *xmin=x;    Add log in  imach.c and  fullversion number is now printed.
       return fx;  
     }  */
     ftemp=fu;  /*
     if (fabs(e) > tol1) {     Interpolated Markov Chain
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    Short summary of the programme:
       p=(x-v)*q-(x-w)*r;    
       q=2.0*(q-r);    This program computes Healthy Life Expectancies from
       if (q > 0.0) p = -p;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
       q=fabs(q);    first survey ("cross") where individuals from different ages are
       etemp=e;    interviewed on their health status or degree of disability (in the
       e=d;    case of a health survey which is our main interest) -2- at least a
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    second wave of interviews ("longitudinal") which measure each change
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    (if any) in individual health status.  Health expectancies are
       else {    computed from the time spent in each health state according to a
         d=p/q;    model. More health states you consider, more time is necessary to reach the
         u=x+d;    Maximum Likelihood of the parameters involved in the model.  The
         if (u-a < tol2 || b-u < tol2)    simplest model is the multinomial logistic model where pij is the
           d=SIGN(tol1,xm-x);    probability to be observed in state j at the second wave
       }    conditional to be observed in state i at the first wave. Therefore
     } else {    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    'age' is age and 'sex' is a covariate. If you want to have a more
     }    complex model than "constant and age", you should modify the program
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    where the markup *Covariates have to be included here again* invites
     fu=(*f)(u);    you to do it.  More covariates you add, slower the
     if (fu <= fx) {    convergence.
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)    The advantage of this computer programme, compared to a simple
         SHFT(fv,fw,fx,fu)    multinomial logistic model, is clear when the delay between waves is not
         } else {    identical for each individual. Also, if a individual missed an
           if (u < x) a=u; else b=u;    intermediate interview, the information is lost, but taken into
           if (fu <= fw || w == x) {    account using an interpolation or extrapolation.  
             v=w;  
             w=u;    hPijx is the probability to be observed in state i at age x+h
             fv=fw;    conditional to the observed state i at age x. The delay 'h' can be
             fw=fu;    split into an exact number (nh*stepm) of unobserved intermediate
           } else if (fu <= fv || v == x || v == w) {    states. This elementary transition (by month, quarter,
             v=u;    semester or year) is modelled as a multinomial logistic.  The hPx
             fv=fu;    matrix is simply the matrix product of nh*stepm elementary matrices
           }    and the contribution of each individual to the likelihood is simply
         }    hPijx.
   }  
   nrerror("Too many iterations in brent");    Also this programme outputs the covariance matrix of the parameters but also
   *xmin=x;    of the life expectancies. It also computes the period (stable) prevalence. 
   return fx;    
 }    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 /****************** mnbrak ***********************/    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    It is copyrighted identically to a GNU software product, ie programme and
             double (*func)(double))    software can be distributed freely for non commercial use. Latest version
 {    can be accessed at http://euroreves.ined.fr/imach .
   double ulim,u,r,q, dum;  
   double fu;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
      or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   *fa=(*func)(*ax);    
   *fb=(*func)(*bx);    **********************************************************************/
   if (*fb > *fa) {  /*
     SHFT(dum,*ax,*bx,dum)    main
       SHFT(dum,*fb,*fa,dum)    read parameterfile
       }    read datafile
   *cx=(*bx)+GOLD*(*bx-*ax);    concatwav
   *fc=(*func)(*cx);    freqsummary
   while (*fb > *fc) {    if (mle >= 1)
     r=(*bx-*ax)*(*fb-*fc);      mlikeli
     q=(*bx-*cx)*(*fb-*fa);    print results files
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    if mle==1 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));       computes hessian
     ulim=(*bx)+GLIMIT*(*cx-*bx);    read end of parameter file: agemin, agemax, bage, fage, estepm
     if ((*bx-u)*(u-*cx) > 0.0) {        begin-prev-date,...
       fu=(*func)(u);    open gnuplot file
     } else if ((*cx-u)*(u-ulim) > 0.0) {    open html file
       fu=(*func)(u);    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
       if (fu < *fc) {     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
           SHFT(*fb,*fc,fu,(*func)(u))      freexexit2 possible for memory heap.
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    h Pij x                         | pij_nom  ficrestpij
       u=ulim;     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
       fu=(*func)(u);         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
     } else {         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
     }         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
     SHFT(*ax,*bx,*cx,u)    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
       SHFT(*fa,*fb,*fc,fu)     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
       }     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
 }  
     forecasting if prevfcast==1 prevforecast call prevalence()
 /*************** linmin ************************/    health expectancies
     Variance-covariance of DFLE
 int ncom;    prevalence()
 double *pcom,*xicom;     movingaverage()
 double (*nrfunc)(double []);    varevsij() 
      if popbased==1 varevsij(,popbased)
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    total life expectancies
 {    Variance of period (stable) prevalence
   double brent(double ax, double bx, double cx,   end
                double (*f)(double), double tol, double *xmin);  */
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  #define POWELL /* Instead of NLOPT */
               double *fc, double (*func)(double));  
   int j;  #include <math.h>
   double xx,xmin,bx,ax;  #include <stdio.h>
   double fx,fb,fa;  #include <stdlib.h>
    #include <string.h>
   ncom=n;  
   pcom=vector(1,n);  #ifdef _WIN32
   xicom=vector(1,n);  #include <io.h>
   nrfunc=func;  #include <windows.h>
   for (j=1;j<=n;j++) {  #include <tchar.h>
     pcom[j]=p[j];  #else
     xicom[j]=xi[j];  #include <unistd.h>
   }  #endif
   ax=0.0;  
   xx=1.0;  #include <limits.h>
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  #include <sys/types.h>
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  #if defined(__GNUC__)
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #include <sys/utsname.h> /* Doesn't work on Windows */
 #endif  #endif
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  #include <sys/stat.h>
     p[j] += xi[j];  #include <errno.h>
   }  /* extern int errno; */
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);  /* #ifdef LINUX */
 }  /* #include <time.h> */
   /* #include "timeval.h" */
 /*************** powell ************************/  /* #else */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  /* #include <sys/time.h> */
             double (*func)(double []))  /* #endif */
 {  
   void linmin(double p[], double xi[], int n, double *fret,  #include <time.h>
               double (*func)(double []));  
   int i,ibig,j;  #ifdef GSL
   double del,t,*pt,*ptt,*xit;  #include <gsl/gsl_errno.h>
   double fp,fptt;  #include <gsl/gsl_multimin.h>
   double *xits;  #endif
   pt=vector(1,n);  
   ptt=vector(1,n);  
   xit=vector(1,n);  #ifdef NLOPT
   xits=vector(1,n);  #include <nlopt.h>
   *fret=(*func)(p);  typedef struct {
   for (j=1;j<=n;j++) pt[j]=p[j];    double (* function)(double [] );
   for (*iter=1;;++(*iter)) {  } myfunc_data ;
     fp=(*fret);  #endif
     ibig=0;  
     del=0.0;  /* #include <libintl.h> */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /* #define _(String) gettext (String) */
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
     printf("\n");  
     for (i=1;i<=n;i++) {  #define GNUPLOTPROGRAM "gnuplot"
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       fptt=(*fret);  #define FILENAMELENGTH 132
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #endif  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
       if (fabs(fptt-(*fret)) > del) {  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
         del=fabs(fptt-(*fret));  
         ibig=i;  #define NINTERVMAX 8
       }  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
 #ifdef DEBUG  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
       printf("%d %.12e",i,(*fret));  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
       for (j=1;j<=n;j++) {  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #define MAXN 20000
         printf(" x(%d)=%.12e",j,xit[j]);  #define YEARM 12. /**< Number of months per year */
       }  #define AGESUP 130
       for(j=1;j<=n;j++)  #define AGEBASE 40
         printf(" p=%.12e",p[j]);  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
       printf("\n");  #ifdef _WIN32
 #endif  #define DIRSEPARATOR '\\'
     }  #define CHARSEPARATOR "\\"
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #define ODIRSEPARATOR '/'
 #ifdef DEBUG  #else
       int k[2],l;  #define DIRSEPARATOR '/'
       k[0]=1;  #define CHARSEPARATOR "/"
       k[1]=-1;  #define ODIRSEPARATOR '\\'
       printf("Max: %.12e",(*func)(p));  #endif
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  /* $Id$ */
       printf("\n");  /* $State$ */
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  char fullversion[]="$Revision$ $Date$"; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  char strstart[80];
         }  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
       }  int nvar=0, nforce=0; /* Number of variables, number of forces */
 #endif  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
       free_vector(xit,1,n);  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
       free_vector(xits,1,n);  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
       free_vector(ptt,1,n);  int cptcovprodnoage=0; /**< Number of covariate products without age */   
       free_vector(pt,1,n);  int cptcoveff=0; /* Total number of covariates to vary for printing results */
       return;  int cptcov=0; /* Working variable */
     }  int npar=NPARMAX;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  int nlstate=2; /* Number of live states */
     for (j=1;j<=n;j++) {  int ndeath=1; /* Number of dead states */
       ptt[j]=2.0*p[j]-pt[j];  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       xit[j]=p[j]-pt[j];  int popbased=0;
       pt[j]=p[j];  
     }  int *wav; /* Number of waves for this individuual 0 is possible */
     fptt=(*func)(ptt);  int maxwav=0; /* Maxim number of waves */
     if (fptt < fp) {  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       if (t < 0.0) {  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
         linmin(p,xit,n,fret,func);                     to the likelihood and the sum of weights (done by funcone)*/
         for (j=1;j<=n;j++) {  int mle=1, weightopt=0;
           xi[j][ibig]=xi[j][n];  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
           xi[j][n]=xit[j];  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
 #ifdef DEBUG             * wave mi and wave mi+1 is not an exact multiple of stepm. */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int countcallfunc=0;  /* Count the number of calls to func */
         for(j=1;j<=n;j++)  double jmean=1; /* Mean space between 2 waves */
           printf(" %.12e",xit[j]);  double **matprod2(); /* test */
         printf("\n");  double **oldm, **newm, **savm; /* Working pointers to matrices */
 #endif  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       }  /*FILE *fic ; */ /* Used in readdata only */
     }  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   }  FILE *ficlog, *ficrespow;
 }  int globpr=0; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
 /**** Prevalence limit ****************/  long ipmx=0; /* Number of contributions */
   double sw; /* Sum of weights */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  char filerespow[FILENAMELENGTH];
 {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  FILE *ficresilk;
      matrix by transitions matrix until convergence is reached */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
   int i, ii,j,k;  FILE *fichtm, *fichtmcov; /* Html File */
   double min, max, maxmin, maxmax,sumnew=0.;  FILE *ficreseij;
   double **matprod2();  char filerese[FILENAMELENGTH];
   double **out, cov[NCOVMAX], **pmij();  FILE *ficresstdeij;
   double **newm;  char fileresstde[FILENAMELENGTH];
   double agefin, delaymax=50 ; /* Max number of years to converge */  FILE *ficrescveij;
   char filerescve[FILENAMELENGTH];
   for (ii=1;ii<=nlstate+ndeath;ii++)  FILE  *ficresvij;
     for (j=1;j<=nlstate+ndeath;j++){  char fileresv[FILENAMELENGTH];
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  FILE  *ficresvpl;
     }  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
    cov[1]=1.;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
    char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  char command[FILENAMELENGTH];
     newm=savm;  int  outcmd=0;
     /* Covariates have to be included here again */  
      cov[2]=agefin;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
    
       for (k=1; k<=cptcovn;k++) {  char filelog[FILENAMELENGTH]; /* Log file */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  char filerest[FILENAMELENGTH];
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  char fileregp[FILENAMELENGTH];
       }  char popfile[FILENAMELENGTH];
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  /* struct timezone tzp; */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  /* extern int gettimeofday(); */
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  struct tm tml, *gmtime(), *localtime();
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
   extern time_t time();
     savm=oldm;  
     oldm=newm;  struct tm start_time, end_time, curr_time, last_time, forecast_time;
     maxmax=0.;  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
     for(j=1;j<=nlstate;j++){  struct tm tm;
       min=1.;  
       max=0.;  char strcurr[80], strfor[80];
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  char *endptr;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  long lval;
         prlim[i][j]= newm[i][j]/(1-sumnew);  double dval;
         max=FMAX(max,prlim[i][j]);  
         min=FMIN(min,prlim[i][j]);  #define NR_END 1
       }  #define FREE_ARG char*
       maxmin=max-min;  #define FTOL 1.0e-10
       maxmax=FMAX(maxmax,maxmin);  
     }  #define NRANSI 
     if(maxmax < ftolpl){  #define ITMAX 200 
       return prlim;  
     }  #define TOL 2.0e-4 
   }  
 }  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 /*************** transition probabilities ***************/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  #define GOLD 1.618034 
 {  #define GLIMIT 100.0 
   double s1, s2;  #define TINY 1.0e-20 
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     for(i=1; i<= nlstate; i++){  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     for(j=1; j<i;j++){    
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
         /*s2 += param[i][j][nc]*cov[nc];*/  #define rint(a) floor(a+0.5)
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  /* #define mytinydouble 1.0e-16 */
       }  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
       ps[i][j]=s2;  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /* static double dsqrarg; */
     }  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
     for(j=i+1; j<=nlstate+ndeath;j++){  static double sqrarg;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  int agegomp= AGEGOMP;
       }  
       ps[i][j]=s2;  int imx; 
     }  int stepm=1;
   }  /* Stepm, step in month: minimum step interpolation*/
     /*ps[3][2]=1;*/  
   int estepm;
   for(i=1; i<= nlstate; i++){  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
      s1=0;  
     for(j=1; j<i; j++)  int m,nb;
       s1+=exp(ps[i][j]);  long *num;
     for(j=i+1; j<=nlstate+ndeath; j++)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       s1+=exp(ps[i][j]);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     ps[i][i]=1./(s1+1.);  double **pmmij, ***probs;
     for(j=1; j<i; j++)  double *ageexmed,*agecens;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  double dateintmean=0;
     for(j=i+1; j<=nlstate+ndeath; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  double *weight;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  int **s; /* Status */
   } /* end i */  double *agedc;
   double  **covar; /**< covar[j,i], value of jth covariate for individual i,
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){                    * covar=matrix(0,NCOVMAX,1,n); 
     for(jj=1; jj<= nlstate+ndeath; jj++){                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       ps[ii][jj]=0;  double  idx; 
       ps[ii][ii]=1;  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
     }  int *Ndum; /** Freq of modality (tricode */
   }  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double *lsurv, *lpop, *tpop;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
      printf("%lf ",ps[ii][jj]);  double ftolhess; /**< Tolerance for computing hessian */
    }  
     printf("\n ");  /**************** split *************************/
     }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     printf("\n ");printf("%lf ",cov[2]);*/  {
 /*    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   for(i=1; i<= npar; i++) printf("%f ",x[i]);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   goto end;*/    */ 
     return ps;    char  *ss;                            /* pointer */
 }    int   l1, l2;                         /* length counters */
   
 /**************** Product of 2 matrices ******************/    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 {    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      strcpy( name, path );               /* we got the fullname name because no directory */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   /* in, b, out are matrice of pointers which should have been initialized        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      before: only the contents of out is modified. The function returns      /* get current working directory */
      a pointer to pointers identical to out */      /*    extern  char* getcwd ( char *buf , int len);*/
   long i, j, k;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   for(i=nrl; i<= nrh; i++)        return( GLOCK_ERROR_GETCWD );
     for(k=ncolol; k<=ncoloh; k++)      }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      /* got dirc from getcwd*/
         out[i][k] +=in[i][j]*b[j][k];      printf(" DIRC = %s \n",dirc);
     } else {                              /* strip direcotry from path */
   return out;      ss++;                               /* after this, the filename */
 }      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
 /************* Higher Matrix Product ***************/      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      printf(" DIRC2 = %s \n",dirc);
 {    }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    /* We add a separator at the end of dirc if not exists */
      duration (i.e. until    l1 = strlen( dirc );                  /* length of directory */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    if( dirc[l1-1] != DIRSEPARATOR ){
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      dirc[l1] =  DIRSEPARATOR;
      (typically every 2 years instead of every month which is too big).      dirc[l1+1] = 0; 
      Model is determined by parameters x and covariates have to be      printf(" DIRC3 = %s \n",dirc);
      included manually here.    }
     ss = strrchr( name, '.' );            /* find last / */
      */    if (ss >0){
       ss++;
   int i, j, d, h, k;      strcpy(ext,ss);                     /* save extension */
   double **out, cov[NCOVMAX];      l1= strlen( name);
   double **newm;      l2= strlen(ss)+1;
       strncpy( finame, name, l1-l2);
   /* Hstepm could be zero and should return the unit matrix */      finame[l1-l2]= 0;
   for (i=1;i<=nlstate+ndeath;i++)    }
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);    return( 0 );                          /* we're done */
       po[i][j][0]=(i==j ? 1.0 : 0.0);  }
     }  
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){  /******************************************/
     for(d=1; d <=hstepm; d++){  
       newm=savm;  void replace_back_to_slash(char *s, char*t)
       /* Covariates have to be included here again */  {
       cov[1]=1.;    int i;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    int lg=0;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    i=0;
       for (k=1; k<=cptcovage;k++)    lg=strlen(t);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    for(i=0; i<= lg; i++) {
       for (k=1; k<=cptcovprod;k++)      (s[i] = t[i]);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      if (t[i]== '\\') s[i]='/';
     }
   }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  char *trimbb(char *out, char *in)
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    char *s;
       savm=oldm;    s=out;
       oldm=newm;    while (*in != '\0'){
     }      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
     for(i=1; i<=nlstate+ndeath; i++)        in++;
       for(j=1;j<=nlstate+ndeath;j++) {      }
         po[i][j][h]=newm[i][j];      *out++ = *in++;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    }
          */    *out='\0';
       }    return s;
   } /* end h */  }
   return po;  
 }  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' 
 /*************** log-likelihood *************/       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
 double func( double *x)       gives blocc="abcdef2ghi" and alocc="j".
 {       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   int i, ii, j, k, mi, d, kk;    */
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    char *s, *t;
   double **out;    t=in;s=in;
   double sw; /* Sum of weights */    while ((*in != occ) && (*in != '\0')){
   double lli; /* Individual log likelihood */      *alocc++ = *in++;
   long ipmx;    }
   /*extern weight */    if( *in == occ){
   /* We are differentiating ll according to initial status */      *(alocc)='\0';
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      s=++in;
   /*for(i=1;i<imx;i++)    }
     printf(" %d\n",s[4][i]);   
   */    if (s == t) {/* occ not found */
   cov[1]=1.;      *(alocc-(in-s))='\0';
       in=s;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    }
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    while ( *in != '\0'){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      *blocc++ = *in++;
     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);    *blocc='\0';
       for(d=0; d<dh[mi][i]; d++){    return t;
         newm=savm;  }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  char *cutv(char *blocc, char *alocc, char *in, char occ)
         for (kk=1; kk<=cptcovage;kk++) {  {
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
         }       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
               gives blocc="abcdef2ghi" and alocc="j".
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,       If occ is not found blocc is null and alocc is equal to in. Returns alocc
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    */
         savm=oldm;    char *s, *t;
         oldm=newm;    t=in;s=in;
            while (*in != '\0'){
              while( *in == occ){
       } /* end mult */        *blocc++ = *in++;
              s=in;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      }
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      *blocc++ = *in++;
       ipmx +=1;    }
       sw += weight[i];    if (s == t) /* occ not found */
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      *(blocc-(in-s))='\0';
     } /* end of wave */    else
   } /* end of individual */      *(blocc-(in-s)-1)='\0';
     in=s;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    while ( *in != '\0'){
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      *alocc++ = *in++;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    }
   return -l;  
 }    *alocc='\0';
     return s;
   }
 /*********** Maximum Likelihood Estimation ***************/  
   int nbocc(char *s, char occ)
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  {
 {    int i,j=0;
   int i,j, iter;    int lg=20;
   double **xi,*delti;    i=0;
   double fret;    lg=strlen(s);
   xi=matrix(1,npar,1,npar);    for(i=0; i<= lg; i++) {
   for (i=1;i<=npar;i++)    if  (s[i] == occ ) j++;
     for (j=1;j<=npar;j++)    }
       xi[i][j]=(i==j ? 1.0 : 0.0);    return j;
   printf("Powell\n");  }
   powell(p,xi,npar,ftol,&iter,&fret,func);  
   /* void cutv(char *u,char *v, char*t, char occ) */
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  /* { */
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
 }  /*      gives u="abcdef2ghi" and v="j" *\/ */
   /*   int i,lg,j,p=0; */
 /**** Computes Hessian and covariance matrix ***/  /*   i=0; */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /*   lg=strlen(t); */
 {  /*   for(j=0; j<=lg-1; j++) { */
   double  **a,**y,*x,pd;  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   double **hess;  /*   } */
   int i, j,jk;  
   int *indx;  /*   for(j=0; j<p; j++) { */
   /*     (u[j] = t[j]); */
   double hessii(double p[], double delta, int theta, double delti[]);  /*   } */
   double hessij(double p[], double delti[], int i, int j);  /*      u[p]='\0'; */
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  /*    for(j=0; j<= lg; j++) { */
   /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   hess=matrix(1,npar,1,npar);  /*   } */
   /* } */
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){  #ifdef _WIN32
     printf("%d",i);fflush(stdout);  char * strsep(char **pp, const char *delim)
     hess[i][i]=hessii(p,ftolhess,i,delti);  {
     /*printf(" %f ",p[i]);*/    char *p, *q;
     /*printf(" %lf ",hess[i][i]);*/           
   }    if ((p = *pp) == NULL)
        return 0;
   for (i=1;i<=npar;i++) {    if ((q = strpbrk (p, delim)) != NULL)
     for (j=1;j<=npar;j++)  {    {
       if (j>i) {      *pp = q + 1;
         printf(".%d%d",i,j);fflush(stdout);      *q = '\0';
         hess[i][j]=hessij(p,delti,i,j);    }
         hess[j][i]=hess[i][j];        else
         /*printf(" %lf ",hess[i][j]);*/      *pp = 0;
       }    return p;
     }  }
   }  #endif
   printf("\n");  
   /********************** nrerror ********************/
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  
    void nrerror(char error_text[])
   a=matrix(1,npar,1,npar);  {
   y=matrix(1,npar,1,npar);    fprintf(stderr,"ERREUR ...\n");
   x=vector(1,npar);    fprintf(stderr,"%s\n",error_text);
   indx=ivector(1,npar);    exit(EXIT_FAILURE);
   for (i=1;i<=npar;i++)  }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  /*********************** vector *******************/
   ludcmp(a,npar,indx,&pd);  double *vector(int nl, int nh)
   {
   for (j=1;j<=npar;j++) {    double *v;
     for (i=1;i<=npar;i++) x[i]=0;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     x[j]=1;    if (!v) nrerror("allocation failure in vector");
     lubksb(a,npar,indx,x);    return v-nl+NR_END;
     for (i=1;i<=npar;i++){  }
       matcov[i][j]=x[i];  
     }  /************************ free vector ******************/
   }  void free_vector(double*v, int nl, int nh)
   {
   printf("\n#Hessian matrix#\n");    free((FREE_ARG)(v+nl-NR_END));
   for (i=1;i<=npar;i++) {  }
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);  /************************ivector *******************************/
     }  int *ivector(long nl,long nh)
     printf("\n");  {
   }    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   /* Recompute Inverse */    if (!v) nrerror("allocation failure in ivector");
   for (i=1;i<=npar;i++)    return v-nl+NR_END;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  }
   ludcmp(a,npar,indx,&pd);  
   /******************free ivector **************************/
   /*  printf("\n#Hessian matrix recomputed#\n");  void free_ivector(int *v, long nl, long nh)
   {
   for (j=1;j<=npar;j++) {    free((FREE_ARG)(v+nl-NR_END));
     for (i=1;i<=npar;i++) x[i]=0;  }
     x[j]=1;  
     lubksb(a,npar,indx,x);  /************************lvector *******************************/
     for (i=1;i<=npar;i++){  long *lvector(long nl,long nh)
       y[i][j]=x[i];  {
       printf("%.3e ",y[i][j]);    long *v;
     }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     printf("\n");    if (!v) nrerror("allocation failure in ivector");
   }    return v-nl+NR_END;
   */  }
   
   free_matrix(a,1,npar,1,npar);  /******************free lvector **************************/
   free_matrix(y,1,npar,1,npar);  void free_lvector(long *v, long nl, long nh)
   free_vector(x,1,npar);  {
   free_ivector(indx,1,npar);    free((FREE_ARG)(v+nl-NR_END));
   free_matrix(hess,1,npar,1,npar);  }
   
   /******************* imatrix *******************************/
 }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 /*************** hessian matrix ****************/  { 
 double hessii( double x[], double delta, int theta, double delti[])    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 {    int **m; 
   int i;    
   int l=1, lmax=20;    /* allocate pointers to rows */ 
   double k1,k2;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   double p2[NPARMAX+1];    if (!m) nrerror("allocation failure 1 in matrix()"); 
   double res;    m += NR_END; 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    m -= nrl; 
   double fx;    
   int k=0,kmax=10;    
   double l1;    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   fx=func(x);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   for (i=1;i<=npar;i++) p2[i]=x[i];    m[nrl] += NR_END; 
   for(l=0 ; l <=lmax; l++){    m[nrl] -= ncl; 
     l1=pow(10,l);    
     delts=delt;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     for(k=1 ; k <kmax; k=k+1){    
       delt = delta*(l1*k);    /* return pointer to array of pointers to rows */ 
       p2[theta]=x[theta] +delt;    return m; 
       k1=func(p2)-fx;  } 
       p2[theta]=x[theta]-delt;  
       k2=func(p2)-fx;  /****************** free_imatrix *************************/
       /*res= (k1-2.0*fx+k2)/delt/delt; */  void free_imatrix(m,nrl,nrh,ncl,nch)
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        int **m;
              long nch,ncl,nrh,nrl; 
 #ifdef DEBUG       /* free an int matrix allocated by imatrix() */ 
       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((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    free((FREE_ARG) (m+nrl-NR_END)); 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  } 
         k=kmax;  
       }  /******************* matrix *******************************/
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  double **matrix(long nrl, long nrh, long ncl, long nch)
         k=kmax; l=lmax*10.;  {
       }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    double **m;
         delts=delt;  
       }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
   }    m += NR_END;
   delti[theta]=delts;    m -= nrl;
   return res;  
      m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 double hessij( double x[], double delti[], int thetai,int thetaj)    m[nrl] -= ncl;
 {  
   int i;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   int l=1, l1, lmax=20;    return m;
   double k1,k2,k3,k4,res,fx;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   double p2[NPARMAX+1];  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   int k;  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
      */
   fx=func(x);  }
   for (k=1; k<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];  /*************************free matrix ************************/
     p2[thetai]=x[thetai]+delti[thetai]/k;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  {
     k1=func(p2)-fx;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      free((FREE_ARG)(m+nrl-NR_END));
     p2[thetai]=x[thetai]+delti[thetai]/k;  }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;  /******************* ma3x *******************************/
    double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     p2[thetai]=x[thetai]-delti[thetai]/k;  {
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     k3=func(p2)-fx;    double ***m;
    
     p2[thetai]=x[thetai]-delti[thetai]/k;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    if (!m) nrerror("allocation failure 1 in matrix()");
     k4=func(p2)-fx;    m += NR_END;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    m -= nrl;
 #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);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 #endif    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   }    m[nrl] += NR_END;
   return res;    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   int i,imax,j,k;    m[nrl][ncl] += NR_END;
   double big,dum,sum,temp;    m[nrl][ncl] -= nll;
   double *vv;    for (j=ncl+1; j<=nch; j++) 
        m[nrl][j]=m[nrl][j-1]+nlay;
   vv=vector(1,n);    
   *d=1.0;    for (i=nrl+1; i<=nrh; i++) {
   for (i=1;i<=n;i++) {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     big=0.0;      for (j=ncl+1; j<=nch; j++) 
     for (j=1;j<=n;j++)        m[i][j]=m[i][j-1]+nlay;
       if ((temp=fabs(a[i][j])) > big) big=temp;    }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    return m; 
     vv[i]=1.0/big;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   for (j=1;j<=n;j++) {    */
     for (i=1;i<j;i++) {  }
       sum=a[i][j];  
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  /*************************free ma3x ************************/
       a[i][j]=sum;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     }  {
     big=0.0;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     for (i=j;i<=n;i++) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       sum=a[i][j];    free((FREE_ARG)(m+nrl-NR_END));
       for (k=1;k<j;k++)  }
         sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  /*************** function subdirf ***********/
       if ( (dum=vv[i]*fabs(sum)) >= big) {  char *subdirf(char fileres[])
         big=dum;  {
         imax=i;    /* Caution optionfilefiname is hidden */
       }    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/"); /* Add to the right */
     if (j != imax) {    strcat(tmpout,fileres);
       for (k=1;k<=n;k++) {    return tmpout;
         dum=a[imax][k];  }
         a[imax][k]=a[j][k];  
         a[j][k]=dum;  /*************** function subdirf2 ***********/
       }  char *subdirf2(char fileres[], char *preop)
       *d = -(*d);  {
       vv[imax]=vv[j];    
     }    /* Caution optionfilefiname is hidden */
     indx[j]=imax;    strcpy(tmpout,optionfilefiname);
     if (a[j][j] == 0.0) a[j][j]=TINY;    strcat(tmpout,"/");
     if (j != n) {    strcat(tmpout,preop);
       dum=1.0/(a[j][j]);    strcat(tmpout,fileres);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    return tmpout;
     }  }
   }  
   free_vector(vv,1,n);  /* Doesn't work */  /*************** function subdirf3 ***********/
 ;  char *subdirf3(char fileres[], char *preop, char *preop2)
 }  {
     
 void lubksb(double **a, int n, int *indx, double b[])    /* Caution optionfilefiname is hidden */
 {    strcpy(tmpout,optionfilefiname);
   int i,ii=0,ip,j;    strcat(tmpout,"/");
   double sum;    strcat(tmpout,preop);
      strcat(tmpout,preop2);
   for (i=1;i<=n;i++) {    strcat(tmpout,fileres);
     ip=indx[i];    return tmpout;
     sum=b[ip];  }
     b[ip]=b[i];  
     if (ii)  char *asc_diff_time(long time_sec, char ascdiff[])
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  {
     else if (sum) ii=i;    long sec_left, days, hours, minutes;
     b[i]=sum;    days = (time_sec) / (60*60*24);
   }    sec_left = (time_sec) % (60*60*24);
   for (i=n;i>=1;i--) {    hours = (sec_left) / (60*60) ;
     sum=b[i];    sec_left = (sec_left) %(60*60);
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    minutes = (sec_left) /60;
     b[i]=sum/a[i][i];    sec_left = (sec_left) % (60);
   }    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
 }    return ascdiff;
   }
 /************ 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)  /***************** f1dim *************************/
 {  /* Some frequencies */  extern int ncom; 
    extern double *pcom,*xicom;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  extern double (*nrfunc)(double []); 
   double ***freq; /* Frequencies */   
   double *pp;  double f1dim(double x) 
   double pos, k2, dateintsum=0,k2cpt=0;  { 
   FILE *ficresp;    int j; 
   char fileresp[FILENAMELENGTH];    double f;
      double *xt; 
   pp=vector(1,nlstate);   
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    xt=vector(1,ncom); 
   strcpy(fileresp,"p");    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   strcat(fileresp,fileres);    f=(*nrfunc)(xt); 
   if((ficresp=fopen(fileresp,"w"))==NULL) {    free_vector(xt,1,ncom); 
     printf("Problem with prevalence resultfile: %s\n", fileresp);    return f; 
     exit(0);  } 
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  /*****************brent *************************/
   j1=0;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
    { 
   j=cptcoveff;    int iter; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    double a,b,d,etemp;
      double fu=0,fv,fw,fx;
   for(k1=1; k1<=j;k1++){    double ftemp=0.;
     for(i1=1; i1<=ncodemax[k1];i1++){    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       j1++;    double e=0.0; 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);   
         scanf("%d", i);*/    a=(ax < cx ? ax : cx); 
       for (i=-1; i<=nlstate+ndeath; i++)      b=(ax > cx ? ax : cx); 
         for (jk=-1; jk<=nlstate+ndeath; jk++)      x=w=v=bx; 
           for(m=agemin; m <= agemax+3; m++)    fw=fv=fx=(*f)(x); 
             freq[i][jk][m]=0;    for (iter=1;iter<=ITMAX;iter++) { 
            xm=0.5*(a+b); 
       dateintsum=0;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       k2cpt=0;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       for (i=1; i<=imx; i++) {      printf(".");fflush(stdout);
         bool=1;      fprintf(ficlog,".");fflush(ficlog);
         if  (cptcovn>0) {  #ifdef DEBUGBRENT
           for (z1=1; z1<=cptcoveff; z1++)      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 (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      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);
               bool=0;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         }  #endif
         if (bool==1) {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
           for(m=firstpass; m<=lastpass; m++){        *xmin=x; 
             k2=anint[m][i]+(mint[m][i]/12.);        return fx; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      } 
               if(agev[m][i]==0) agev[m][i]=agemax+1;      ftemp=fu;
               if(agev[m][i]==1) agev[m][i]=agemax+2;      if (fabs(e) > tol1) { 
               if (m<lastpass) {        r=(x-w)*(fx-fv); 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        q=(x-v)*(fx-fw); 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        p=(x-v)*q-(x-w)*r; 
               }        q=2.0*(q-r); 
                      if (q > 0.0) p = -p; 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        q=fabs(q); 
                 dateintsum=dateintsum+k2;        etemp=e; 
                 k2cpt++;        e=d; 
               }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
             }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           }        else { 
         }          d=p/q; 
       }          u=x+d; 
                  if (u-a < tol2 || b-u < tol2) 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            d=SIGN(tol1,xm-x); 
         } 
       if  (cptcovn>0) {      } else { 
         fprintf(ficresp, "\n#********** Variable ");        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      } 
         fprintf(ficresp, "**********\n#");      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       }      fu=(*f)(u); 
       for(i=1; i<=nlstate;i++)      if (fu <= fx) { 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        if (u >= x) a=x; else b=x; 
       fprintf(ficresp, "\n");        SHFT(v,w,x,u) 
                SHFT(fv,fw,fx,fu) 
       for(i=(int)agemin; i <= (int)agemax+3; i++){          } else { 
         if(i==(int)agemax+3)            if (u < x) a=u; else b=u; 
           printf("Total");            if (fu <= fw || w == x) { 
         else              v=w; 
           printf("Age %d", i);              w=u; 
         for(jk=1; jk <=nlstate ; jk++){              fv=fw; 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              fw=fu; 
             pp[jk] += freq[jk][m][i];            } else if (fu <= fv || v == x || v == w) { 
         }              v=u; 
         for(jk=1; jk <=nlstate ; jk++){              fv=fu; 
           for(m=-1, pos=0; m <=0 ; m++)            } 
             pos += freq[jk][m][i];          } 
           if(pp[jk]>=1.e-10)    } 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    nrerror("Too many iterations in brent"); 
           else    *xmin=x; 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    return fx; 
         }  } 
   
         for(jk=1; jk <=nlstate ; jk++){  /****************** mnbrak ***********************/
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
             pp[jk] += freq[jk][m][i];  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         }              double (*func)(double)) 
   { 
         for(jk=1,pos=0; jk <=nlstate ; jk++)    double ulim,u,r,q, dum;
           pos += pp[jk];    double fu; 
         for(jk=1; jk <=nlstate ; jk++){   
           if(pos>=1.e-5)    *fa=(*func)(*ax); 
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    *fb=(*func)(*bx); 
           else    if (*fb > *fa) { 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      SHFT(dum,*ax,*bx,dum) 
           if( i <= (int) agemax){        SHFT(dum,*fb,*fa,dum) 
             if(pos>=1.e-5){        } 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    *cx=(*bx)+GOLD*(*bx-*ax); 
               probs[i][jk][j1]= pp[jk]/pos;    *fc=(*func)(*cx); 
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    while (*fb > *fc) { /* Declining fa, fb, fc */
             }      r=(*bx-*ax)*(*fb-*fc); 
             else      q=(*bx-*cx)*(*fb-*fa); 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
           }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
         }      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
              if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
         for(jk=-1; jk <=nlstate+ndeath; jk++)        fu=(*func)(u); 
           for(m=-1; m <=nlstate+ndeath; m++)  #ifdef DEBUG
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        /* f(x)=A(x-u)**2+f(u) */
         if(i <= (int) agemax)        double A, fparabu; 
           fprintf(ficresp,"\n");        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
         printf("\n");        fparabu= *fa - A*(*ax-u)*(*ax-u);
       }        printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
     }        fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
   }  #endif 
   dateintmean=dateintsum/k2cpt;      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
          fu=(*func)(u); 
   fclose(ficresp);        if (fu < *fc) { 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   free_vector(pp,1,nlstate);            SHFT(*fb,*fc,fu,(*func)(u)) 
              } 
   /* End of Freq */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
 }        u=ulim; 
         fu=(*func)(u); 
 /************ Prevalence ********************/      } else { 
 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)        u=(*cx)+GOLD*(*cx-*bx); 
 {  /* Some frequencies */        fu=(*func)(u); 
        } 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      SHFT(*ax,*bx,*cx,u) 
   double ***freq; /* Frequencies */        SHFT(*fa,*fb,*fc,fu) 
   double *pp;        } 
   double pos, k2;  } 
   
   pp=vector(1,nlstate);  /*************** linmin ************************/
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
    resets p to where the function func(p) takes on a minimum along the direction xi from p ,
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
   j1=0;  the value of func at the returned location p . This is actually all accomplished by calling the
    routines mnbrak and brent .*/
   j=cptcoveff;  int ncom; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  double *pcom,*xicom;
    double (*nrfunc)(double []); 
  for(k1=1; k1<=j;k1++){   
     for(i1=1; i1<=ncodemax[k1];i1++){  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       j1++;  { 
      double brent(double ax, double bx, double cx, 
       for (i=-1; i<=nlstate+ndeath; i++)                   double (*f)(double), double tol, double *xmin); 
         for (jk=-1; jk<=nlstate+ndeath; jk++)      double f1dim(double x); 
           for(m=agemin; m <= agemax+3; m++)    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
             freq[i][jk][m]=0;                double *fc, double (*func)(double)); 
          int j; 
       for (i=1; i<=imx; i++) {    double xx,xmin,bx,ax; 
         bool=1;    double fx,fb,fa;
         if  (cptcovn>0) {   
           for (z1=1; z1<=cptcoveff; z1++)    ncom=n; 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    pcom=vector(1,n); 
               bool=0;    xicom=vector(1,n); 
         }    nrfunc=func; 
         if (bool==1) {    for (j=1;j<=n;j++) { 
           for(m=firstpass; m<=lastpass; m++){      pcom[j]=p[j]; 
             k2=anint[m][i]+(mint[m][i]/12.);      xicom[j]=xi[j]; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    } 
               if(agev[m][i]==0) agev[m][i]=agemax+1;    ax=0.0; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    xx=1.0; 
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
             }  #ifdef DEBUG
           }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       }  #endif
         for(i=(int)agemin; i <= (int)agemax+3; i++){    for (j=1;j<=n;j++) { 
           for(jk=1; jk <=nlstate ; jk++){      xi[j] *= xmin; 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      p[j] += xi[j]; 
               pp[jk] += freq[jk][m][i];    } 
           }    free_vector(xicom,1,n); 
           for(jk=1; jk <=nlstate ; jk++){    free_vector(pcom,1,n); 
             for(m=-1, pos=0; m <=0 ; m++)  } 
             pos += freq[jk][m][i];  
         }  
          /*************** powell ************************/
          for(jk=1; jk <=nlstate ; jk++){  /*
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  Minimization of a function func of n variables. Input consists of an initial starting point
              pp[jk] += freq[jk][m][i];  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
          }  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
            such that failure to decrease by more than this amount on one iteration signals doneness. On
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
   function value at p , and iter is the number of iterations taken. The routine linmin is used.
          for(jk=1; jk <=nlstate ; jk++){             */
            if( i <= (int) agemax){  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
              if(pos>=1.e-5){              double (*func)(double [])) 
                probs[i][jk][j1]= pp[jk]/pos;  { 
              }    void linmin(double p[], double xi[], int n, double *fret, 
            }                double (*func)(double [])); 
          }    int i,ibig,j; 
              double del,t,*pt,*ptt,*xit;
         }    double fp,fptt;
     }    double *xits;
   }    int niterf, itmp;
    
      pt=vector(1,n); 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    ptt=vector(1,n); 
   free_vector(pp,1,nlstate);    xit=vector(1,n); 
      xits=vector(1,n); 
 }  /* End of Freq */    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
 /************* Waves Concatenation ***************/      rcurr_time = time(NULL);  
     for (*iter=1;;++(*iter)) { 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      fp=(*fret); 
 {      ibig=0; 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      del=0.0; 
      Death is a valid wave (if date is known).      rlast_time=rcurr_time;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      /* (void) gettimeofday(&curr_time,&tzp); */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      rcurr_time = time(NULL);  
      and mw[mi+1][i]. dh depends on stepm.      curr_time = *localtime(&rcurr_time);
      */      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
   int i, mi, m;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;     for (i=1;i<=n;i++) {
      double sum=0., jmean=0.;*/        printf(" %d %.12f",i, p[i]);
         fprintf(ficlog," %d %.12lf",i, p[i]);
   int j, k=0,jk, ju, jl;        fprintf(ficrespow," %.12lf", p[i]);
   double sum=0.;      }
   jmin=1e+5;      printf("\n");
   jmax=-1;      fprintf(ficlog,"\n");
   jmean=0.;      fprintf(ficrespow,"\n");fflush(ficrespow);
   for(i=1; i<=imx; i++){      if(*iter <=3){
     mi=0;        tml = *localtime(&rcurr_time);
     m=firstpass;        strcpy(strcurr,asctime(&tml));
     while(s[m][i] <= nlstate){        rforecast_time=rcurr_time; 
       if(s[m][i]>=1)        itmp = strlen(strcurr);
         mw[++mi][i]=m;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
       if(m >=lastpass)          strcurr[itmp-1]='\0';
         break;        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       else        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
         m++;        for(niterf=10;niterf<=30;niterf+=10){
     }/* end while */          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
     if (s[m][i] > nlstate){          forecast_time = *localtime(&rforecast_time);
       mi++;     /* Death is another wave */          strcpy(strfor,asctime(&forecast_time));
       /* if(mi==0)  never been interviewed correctly before death */          itmp = strlen(strfor);
          /* Only death is a correct wave */          if(strfor[itmp-1]=='\n')
       mw[mi][i]=m;          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);
           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);
     wav[i]=mi;        }
     if(mi==0)      }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      for (i=1;i<=n;i++) { 
   }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
   for(i=1; i<=imx; i++){  #ifdef DEBUG
     for(mi=1; mi<wav[i];mi++){            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
       if (stepm <=0)            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
         dh[mi][i]=1;  #endif
       else{        printf("%d",i);fflush(stdout);
         if (s[mw[mi+1][i]][i] > nlstate) {        fprintf(ficlog,"%d",i);fflush(ficlog);
           if (agedc[i] < 2*AGESUP) {        linmin(p,xit,n,fret,func); 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        if (fabs(fptt-(*fret)) > del) { 
           if(j==0) j=1;  /* Survives at least one month after exam */          del=fabs(fptt-(*fret)); 
           k=k+1;          ibig=i; 
           if (j >= jmax) jmax=j;        } 
           if (j <= jmin) jmin=j;  #ifdef DEBUG
           sum=sum+j;        printf("%d %.12e",i,(*fret));
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        fprintf(ficlog,"%d %.12e",i,(*fret));
           }        for (j=1;j<=n;j++) {
         }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         else{          printf(" x(%d)=%.12e",j,xit[j]);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
           k=k+1;        }
           if (j >= jmax) jmax=j;        for(j=1;j<=n;j++) {
           else if (j <= jmin)jmin=j;          printf(" p(%d)=%.12e",j,p[j]);
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
           sum=sum+j;        }
         }        printf("\n");
         jk= j/stepm;        fprintf(ficlog,"\n");
         jl= j -jk*stepm;  #endif
         ju= j -(jk+1)*stepm;      } /* end i */
         if(jl <= -ju)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
           dh[mi][i]=jk;  #ifdef DEBUG
         else        int k[2],l;
           dh[mi][i]=jk+1;        k[0]=1;
         if(dh[mi][i]==0)        k[1]=-1;
           dh[mi][i]=1; /* At least one step */        printf("Max: %.12e",(*func)(p));
       }        fprintf(ficlog,"Max: %.12e",(*func)(p));
     }        for (j=1;j<=n;j++) {
   }          printf(" %.12e",p[j]);
   jmean=sum/k;          fprintf(ficlog," %.12e",p[j]);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        }
  }        printf("\n");
 /*********** Tricode ****************************/        fprintf(ficlog,"\n");
 void tricode(int *Tvar, int **nbcode, int imx)        for(l=0;l<=1;l++) {
 {          for (j=1;j<=n;j++) {
   int Ndum[20],ij=1, k, j, i;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   int cptcode=0;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   cptcoveff=0;            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 (k=0; k<19; k++) Ndum[k]=0;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for (k=1; k<=7; k++) ncodemax[k]=0;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  #endif
     for (i=1; i<=imx; i++) {  
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;        free_vector(xit,1,n); 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        free_vector(xits,1,n); 
       if (ij > cptcode) cptcode=ij;        free_vector(ptt,1,n); 
     }        free_vector(pt,1,n); 
         return; 
     for (i=0; i<=cptcode; i++) {      } 
       if(Ndum[i]!=0) ncodemax[j]++;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     }      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
     ij=1;        ptt[j]=2.0*p[j]-pt[j]; 
         xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
     for (i=1; i<=ncodemax[j]; i++) {      } 
       for (k=0; k<=19; k++) {      fptt=(*func)(ptt); 
         if (Ndum[k] != 0) {      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
           nbcode[Tvar[j]][ij]=k;        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
           ij++;        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
         }        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
         if (ij > ncodemax[j]) break;        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
       }          /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
     }        /* Thus we compare delta(2h) with observed f1-f3 */
   }          /* or best gain on one ancient line 'del' with total  */
         /* gain f1-f2 = f1 - f2 - 'del' with del  */
  for (k=0; k<19; k++) Ndum[k]=0;        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   
  for (i=1; i<=ncovmodel-2; i++) {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
       ij=Tvar[i];        t= t- del*SQR(fp-fptt);
       Ndum[ij]++;        printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
     }        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
   #ifdef DEBUG
  ij=1;        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
  for (i=1; i<=10; i++) {               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
    if((Ndum[i]!=0) && (i<=ncovcol)){        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
      Tvaraff[ij]=i;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
      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);
  }  #endif
          if (t < 0.0) { /* Then we use it for last direction */
     cptcoveff=ij-1;          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
 }          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
 /*********** Health Expectancies ****************/            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
           }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
 {          fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h, nstepm;  #ifdef DEBUG
   double age, agelim, hf;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double ***p3mat;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
            for(j=1;j<=n;j++){
   fprintf(ficreseij,"# Health expectancies\n");            printf(" %.12e",xit[j]);
   fprintf(ficreseij,"# Age");            fprintf(ficlog," %.12e",xit[j]);
   for(i=1; i<=nlstate;i++)          }
     for(j=1; j<=nlstate;j++)          printf("\n");
       fprintf(ficreseij," %1d-%1d",i,j);          fprintf(ficlog,"\n");
   fprintf(ficreseij,"\n");  #endif
         } /* end of t negative */
   if(estepm < stepm){      } /* end if (fptt < fp)  */
     printf ("Problem %d lower than %d\n",estepm, stepm);    } 
   }  } 
   else  hstepm=estepm;    
   /* We compute the life expectancy from trapezoids spaced every estepm months  /**** Prevalence limit (stable or period prevalence)  ****************/
    * 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  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
    * we are calculating an estimate of the Life Expectancy assuming a linear  {
    * progression inbetween and thus overestimating or underestimating according    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
    * to the curvature of the survival function. If, for the same date, we       matrix by transitions matrix until convergence is reached */
    * 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    int i, ii,j,k;
    * hypothesis. A more precise result, taking into account a more precise    double min, max, maxmin, maxmax,sumnew=0.;
    * curvature will be obtained if estepm is as small as stepm. */    /* double **matprod2(); */ /* test */
     double **out, cov[NCOVMAX+1], **pmij();
   /* For example we decided to compute the life expectancy with the smallest unit */    double **newm;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    double agefin, delaymax=50 ; /* Max number of years to converge */
      nhstepm is the number of hstepm from age to agelim    
      nstepm is the number of stepm from age to agelin.    for (ii=1;ii<=nlstate+ndeath;ii++)
      Look at hpijx to understand the reason of that which relies in memory size      for (j=1;j<=nlstate+ndeath;j++){
      and note for a fixed period like estepm months */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* 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    cov[1]=1.;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    
      results. So we changed our mind and took the option of the best precision.    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   */    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      newm=savm;
       /* Covariates have to be included here again */
   agelim=AGESUP;      cov[2]=agefin;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      
     /* nhstepm age range expressed in number of stepm */      for (k=1; k<=cptcovn;k++) {
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */        /*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]]);*/
     /* if (stepm >= YEARM) hstepm=1;*/      }
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     for(i=1; i<=nlstate;i++)      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       for(j=1; j<=nlstate;j++)      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
           /* 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]);*/      
         }      savm=oldm;
     fprintf(ficreseij,"%3.0f",age );      oldm=newm;
     for(i=1; i<=nlstate;i++)      maxmax=0.;
       for(j=1; j<=nlstate;j++){      for(j=1;j<=nlstate;j++){
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);        min=1.;
       }        max=0.;
     fprintf(ficreseij,"\n");        for(i=1; i<=nlstate; i++) {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          sumnew=0;
   }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 }          prlim[i][j]= newm[i][j]/(1-sumnew);
           /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
 /************ Variance ******************/          max=FMAX(max,prlim[i][j]);
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)          min=FMIN(min,prlim[i][j]);
 {        }
   /* Variance of health expectancies */        maxmin=max-min;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        maxmax=FMAX(maxmax,maxmin);
   double **newm;      } /* j loop */
   double **dnewm,**doldm;      if(maxmax < ftolpl){
   int i, j, nhstepm, hstepm, h, nstepm ;        return prlim;
   int k, cptcode;      }
   double *xp;    } /* age loop */
   double **gp, **gm;    return prlim; /* should not reach here */
   double ***gradg, ***trgradg;  }
   double ***p3mat;  
   double age,agelim, hf;  /*************** transition probabilities ***************/ 
   int theta;  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
    fprintf(ficresvij,"# Covariances of life expectancies\n");  {
   fprintf(ficresvij,"# Age");    /* According to parameters values stored in x and the covariate's values stored in cov,
   for(i=1; i<=nlstate;i++)       computes the probability to be observed in state j being in state i by appying the
     for(j=1; j<=nlstate;j++)       model to the ncovmodel covariates (including constant and age).
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
   fprintf(ficresvij,"\n");       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
        ncth covariate in the global vector x is given by the formula:
   xp=vector(1,npar);       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
   dnewm=matrix(1,nlstate,1,npar);       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
   doldm=matrix(1,nlstate,1,nlstate);       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
         sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
   if(estepm < stepm){       Outputs ps[i][j] the probability to be observed in j being in j according to
     printf ("Problem %d lower than %d\n",estepm, stepm);       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   }    */
   else  hstepm=estepm;      double s1, lnpijopii;
   /* For example we decided to compute the life expectancy with the smallest unit */    /*double t34;*/
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    int i,j, nc, ii, jj;
      nhstepm is the number of hstepm from age to agelim  
      nstepm is the number of stepm from age to agelin.      for(i=1; i<= nlstate; i++){
      Look at hpijx to understand the reason of that which relies in memory size        for(j=1; j<i;j++){
      and note for a fixed period like k years */          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            /*lnpijopii += param[i][j][nc]*cov[nc];*/
      survival function given by stepm (the optimization length). Unfortunately it            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
      means that if the survival funtion is printed only each two years of age and if  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
      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.          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   */  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        }
   agelim = AGESUP;        for(j=i+1; j<=nlstate+ndeath;j++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          }
     gp=matrix(0,nhstepm,1,nlstate);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     gm=matrix(0,nhstepm,1,nlstate);        }
       }
     for(theta=1; theta <=npar; theta++){      
       for(i=1; i<=npar; i++){ /* Computes gradient */      for(i=1; i<= nlstate; i++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        s1=0;
       }        for(j=1; j<i; j++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }
       if (popbased==1) {        for(j=i+1; j<=nlstate+ndeath; j++){
         for(i=1; i<=nlstate;i++)          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           prlim[i][i]=probs[(int)age][i][ij];          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       }        }
          /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       for(j=1; j<= nlstate; j++){        ps[i][i]=1./(s1+1.);
         for(h=0; h<=nhstepm; h++){        /* Computing other pijs */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        for(j=1; j<i; j++)
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          ps[i][j]= exp(ps[i][j])*ps[i][i];
         }        for(j=i+1; j<=nlstate+ndeath; j++)
       }          ps[i][j]= exp(ps[i][j])*ps[i][i];
            /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       for(i=1; i<=npar; i++) /* Computes gradient */      } /* end i */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for(jj=1; jj<= nlstate+ndeath; jj++){
            ps[ii][jj]=0;
       if (popbased==1) {          ps[ii][ii]=1;
         for(i=1; i<=nlstate;i++)        }
           prlim[i][i]=probs[(int)age][i][ij];      }
       }      
       
       for(j=1; j<= nlstate; j++){      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
         for(h=0; h<=nhstepm; h++){      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      /*   } */
         }      /*   printf("\n "); */
       }      /* } */
       /* printf("\n ");printf("%lf ",cov[2]);*/
       for(j=1; j<= nlstate; j++)      /*
         for(h=0; h<=nhstepm; h++){        for(i=1; i<= npar; i++) printf("%f ",x[i]);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        goto end;*/
         }      return ps;
     } /* End theta */  }
   
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  /**************** Product of 2 matrices ******************/
   
     for(h=0; h<=nhstepm; h++)  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
       for(j=1; j<=nlstate;j++)  {
         for(theta=1; theta <=npar; theta++)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
           trgradg[h][j][theta]=gradg[h][theta][j];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */       before: only the contents of out is modified. The function returns
     for(i=1;i<=nlstate;i++)       a pointer to pointers identical to out */
       for(j=1;j<=nlstate;j++)    int i, j, k;
         vareij[i][j][(int)age] =0.;    for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++){
     for(h=0;h<=nhstepm;h++){        out[i][k]=0.;
       for(k=0;k<=nhstepm;k++){        for(j=ncl; j<=nch; j++)
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          out[i][k] +=in[i][j]*b[j][k];
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      }
         for(i=1;i<=nlstate;i++)    return out;
           for(j=1;j<=nlstate;j++)  }
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;  
       }  
     }  /************* Higher Matrix Product ***************/
   
     fprintf(ficresvij,"%.0f ",age );  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     for(i=1; i<=nlstate;i++)  {
       for(j=1; j<=nlstate;j++){    /* Computes the transition matrix starting at age 'age' over 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);       'nhstepm*hstepm*stepm' months (i.e. until
       }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     fprintf(ficresvij,"\n");       nhstepm*hstepm matrices. 
     free_matrix(gp,0,nhstepm,1,nlstate);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     free_matrix(gm,0,nhstepm,1,nlstate);       (typically every 2 years instead of every month which is too big 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);       for the memory).
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);       Model is determined by parameters x and covariates have to be 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       included manually here. 
   } /* End age */  
         */
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);    int i, j, d, h, k;
   free_matrix(dnewm,1,nlstate,1,nlstate);    double **out, cov[NCOVMAX+1];
     double **newm;
 }  
     /* Hstepm could be zero and should return the unit matrix */
 /************ Variance of prevlim ******************/    for (i=1;i<=nlstate+ndeath;i++)
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)      for (j=1;j<=nlstate+ndeath;j++){
 {        oldm[i][j]=(i==j ? 1.0 : 0.0);
   /* Variance of prevalence limit */        po[i][j][0]=(i==j ? 1.0 : 0.0);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      }
   double **newm;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   double **dnewm,**doldm;    for(h=1; h <=nhstepm; h++){
   int i, j, nhstepm, hstepm;      for(d=1; d <=hstepm; d++){
   int k, cptcode;        newm=savm;
   double *xp;        /* Covariates have to be included here again */
   double *gp, *gm;        cov[1]=1.;
   double **gradg, **trgradg;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double age,agelim;        for (k=1; k<=cptcovn;k++) 
   int theta;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
            for (k=1; k<=cptcovage;k++)
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   fprintf(ficresvpl,"# Age");        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   for(i=1; i<=nlstate;i++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   xp=vector(1,npar);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   dnewm=matrix(1,nlstate,1,npar);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   doldm=matrix(1,nlstate,1,nlstate);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
          savm=oldm;
   hstepm=1*YEARM; /* Every year of age */        oldm=newm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      }
   agelim = AGESUP;      for(i=1; i<=nlstate+ndeath; i++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        for(j=1;j<=nlstate+ndeath;j++) {
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          po[i][j][h]=newm[i][j];
     if (stepm >= YEARM) hstepm=1;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        }
     gradg=matrix(1,npar,1,nlstate);      /*printf("h=%d ",h);*/
     gp=vector(1,nlstate);    } /* end h */
     gm=vector(1,nlstate);  /*     printf("\n H=%d \n",h); */
     return po;
     for(theta=1; theta <=npar; theta++){  }
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  #ifdef NLOPT
       }    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double fret;
       for(i=1;i<=nlstate;i++)    double *xt;
         gp[i] = prlim[i][i];    int j;
        myfunc_data *d2 = (myfunc_data *) pd;
       for(i=1; i<=npar; i++) /* Computes gradient */  /* xt = (p1-1); */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    xt=vector(1,n); 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
       for(i=1;i<=nlstate;i++)  
         gm[i] = prlim[i][i];    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
     /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
       for(i=1;i<=nlstate;i++)    printf("Function = %.12lf ",fret);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     } /* End theta */    printf("\n");
    free_vector(xt,1,n);
     trgradg =matrix(1,nlstate,1,npar);    return fret;
   }
     for(j=1; j<=nlstate;j++)  #endif
       for(theta=1; theta <=npar; theta++)  
         trgradg[j][theta]=gradg[theta][j];  /*************** log-likelihood *************/
   double func( double *x)
     for(i=1;i<=nlstate;i++)  {
       varpl[i][(int)age] =0.;    int i, ii, j, k, mi, d, kk;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    double **out;
     for(i=1;i<=nlstate;i++)    double sw; /* Sum of weights */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    double lli; /* Individual log likelihood */
     int s1, s2;
     fprintf(ficresvpl,"%.0f ",age );    double bbh, survp;
     for(i=1; i<=nlstate;i++)    long ipmx;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    /*extern weight */
     fprintf(ficresvpl,"\n");    /* We are differentiating ll according to initial status */
     free_vector(gp,1,nlstate);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     free_vector(gm,1,nlstate);    /*for(i=1;i<imx;i++) 
     free_matrix(gradg,1,npar,1,nlstate);      printf(" %d\n",s[4][i]);
     free_matrix(trgradg,1,nlstate,1,npar);    */
   } /* End age */  
     ++countcallfunc;
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);    cov[1]=1.;
   free_matrix(dnewm,1,nlstate,1,nlstate);  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
 }  
     if(mle==1){
 /************ Variance of one-step probabilities  ******************/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        /* Computes the values of the ncovmodel covariates of the model
 {           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
   int i, j;           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
   int k=0, cptcode;           to be observed in j being in i according to the model.
   double **dnewm,**doldm;         */
   double *xp;        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
   double *gp, *gm;          cov[2+k]=covar[Tvar[k]][i];
   double **gradg, **trgradg;        }
   double age,agelim, cov[NCOVMAX];        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
   int theta;           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
   char fileresprob[FILENAMELENGTH];           has been calculated etc */
         for(mi=1; mi<= wav[i]-1; mi++){
   strcpy(fileresprob,"prob");          for (ii=1;ii<=nlstate+ndeath;ii++)
   strcat(fileresprob,fileres);            for (j=1;j<=nlstate+ndeath;j++){
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("Problem with resultfile: %s\n", fileresprob);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   xp=vector(1,npar);            for (kk=1; kk<=cptcovage;kk++) {
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            }
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   cov[1]=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (age=bage; age<=fage; age ++){            savm=oldm;
     cov[2]=age;            oldm=newm;
     gradg=matrix(1,npar,1,9);          } /* end mult */
     trgradg=matrix(1,9,1,npar);        
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          /* But now since version 0.9 we anticipate for bias at large stepm.
               * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for(theta=1; theta <=npar; theta++){           * (in months) between two waves is not a multiple of stepm, we rounded to 
       for(i=1; i<=npar; i++)           * the nearest (and in case of equal distance, to the lowest) interval but now
         xp[i] = x[i] + (i==theta ?delti[theta]:0);           * 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
       pmij(pmmij,cov,ncovmodel,xp,nlstate);           * probability in order to take into account the bias as a fraction of the way
               * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       k=0;           * -stepm/2 to stepm/2 .
       for(i=1; i<= (nlstate+ndeath); i++){           * For stepm=1 the results are the same as for previous versions of Imach.
         for(j=1; j<=(nlstate+ndeath);j++){           * For stepm > 1 the results are less biased than in previous versions. 
            k=k+1;           */
           gp[k]=pmmij[i][j];          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
       }          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias bh is positive if real duration
       for(i=1; i<=npar; i++)           * is higher than the multiple of stepm and negative otherwise.
         xp[i] = x[i] - (i==theta ?delti[theta]:0);           */
              /* 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){ 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            /* i.e. if s2 is a death state and if the date of death is known 
       k=0;               then the contribution to the likelihood is the probability to 
       for(i=1; i<=(nlstate+ndeath); i++){               die between last step unit time and current  step unit time, 
         for(j=1; j<=(nlstate+ndeath);j++){               which is also equal to probability to die before dh 
           k=k+1;               minus probability to die before dh-stepm . 
           gm[k]=pmmij[i][j];               In version up to 0.92 likelihood was computed
         }          as if date of death was unknown. Death was treated as any other
       }          health state: the date of the interview describes the actual state
                and not the date of a change in health state. The former idea was
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          to consider that at each interview the state was recorded
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            (healthy, disable or death) and IMaCh was corrected; but when we
     }          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          contribution is smaller and very dependent of the step unit
       for(theta=1; theta <=npar; theta++)          stepm. It is no more the probability to die between last interview
       trgradg[j][theta]=gradg[theta][j];          and month of death but the probability to survive from last
            interview up to one month before death multiplied by the
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          probability to die within a month. Thanks to Chris
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
      pmij(pmmij,cov,ncovmodel,x,nlstate);          which slows down the processing. The difference can be up to 10%
           lower mortality.
      k=0;            */
      for(i=1; i<=(nlstate+ndeath); i++){            lli=log(out[s1][s2] - savm[s1][s2]);
        for(j=1; j<=(nlstate+ndeath);j++){  
          k=k+1;  
          gm[k]=pmmij[i][j];          } else if  (s2==-2) {
         }            for (j=1,survp=0. ; j<=nlstate; j++) 
      }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                  /*survp += out[s1][j]; */
      /*printf("\n%d ",(int)age);            lli= log(survp);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          }
                  
           else if  (s2==-4) { 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            for (j=3,survp=0. ; j<=nlstate; j++)  
      }*/              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
   fprintf(ficresprob,"\n%d ",(int)age);          } 
   
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          else if  (s2==-5) { 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            for (j=1,survp=0. ; j<=2; j++)  
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   }            lli= log(survp); 
           } 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          else{
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            /*  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 */
 }          } 
  free_vector(xp,1,npar);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 fclose(ficresprob);          /*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;
           sw += weight[i];
 /******************* Printing html file ***********/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \        } /* end of wave */
  int lastpass, int stepm, int weightopt, char model[],\      } /* end of individual */
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    }  else if(mle==2){
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
  char version[], int popforecast, int estepm ){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int jj1, k1, i1, cpt;        for(mi=1; mi<= wav[i]-1; mi++){
   FILE *fichtm;          for (ii=1;ii<=nlstate+ndeath;ii++)
   /*char optionfilehtm[FILENAMELENGTH];*/            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcpy(optionfilehtm,optionfile);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcat(optionfilehtm,".htm");            }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          for(d=0; d<=dh[mi][i]; d++){
     printf("Problem with %s \n",optionfilehtm), exit(0);            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n            }
 \n            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 Total number of observations=%d <br>\n                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n            savm=oldm;
 <hr  size=\"2\" color=\"#EC5E5E\">            oldm=newm;
  <ul><li>Outputs files<br>\n          } /* end mult */
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n          s1=s[mw[mi][i]][i];
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          s2=s[mw[mi+1][i]][i];
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n          bbh=(double)bh[mi][i]/(double)stepm; 
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n          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 */
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,estepm);          ipmx +=1;
           sw += weight[i];
  fprintf(fichtm,"\n          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n        } /* end of wave */
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      } /* end of individual */
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n    }  else if(mle==3){  /* exponential inter-extrapolation */
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
  if(popforecast==1) fprintf(fichtm,"\n        for(mi=1; mi<= wav[i]-1; mi++){
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n          for (ii=1;ii<=nlstate+ndeath;ii++)
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n            for (j=1;j<=nlstate+ndeath;j++){
         <br>",fileres,fileres,fileres,fileres);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  else              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    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);            }
 fprintf(fichtm," <li>Graphs</li><p>");          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
  m=cptcoveff;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
  jj1=0;            }
  for(k1=1; k1<=m;k1++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
    for(i1=1; i1<=ncodemax[k1];i1++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
        jj1++;            savm=oldm;
        if (cptcovn > 0) {            oldm=newm;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          } /* end mult */
          for (cpt=1; cpt<=cptcoveff;cpt++)        
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          s1=s[mw[mi][i]][i];
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          s2=s[mw[mi+1][i]][i];
        }          bbh=(double)bh[mi][i]/(double)stepm; 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          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 */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              ipmx +=1;
        for(cpt=1; cpt<nlstate;cpt++){          sw += weight[i];
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        } /* end of wave */
        }      } /* end of individual */
     for(cpt=1; cpt<=nlstate;cpt++) {    }else if (mle==4){  /* ml=4 no inter-extrapolation */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 interval) in state (%d): v%s%d%d.gif <br>        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for(mi=1; mi<= wav[i]-1; mi++){
      }          for (ii=1;ii<=nlstate+ndeath;ii++)
      for(cpt=1; cpt<=nlstate;cpt++) {            for (j=1;j<=nlstate+ndeath;j++){
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      }            }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          for(d=0; d<dh[mi][i]; d++){
 health expectancies in states (1) and (2): e%s%d.gif<br>            newm=savm;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 fprintf(fichtm,"\n</body>");            for (kk=1; kk<=cptcovage;kk++) {
    }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
    }            }
 fclose(fichtm);          
 }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /******************* Gnuplot file **************/            savm=oldm;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){            oldm=newm;
           } /* end mult */
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        
           s1=s[mw[mi][i]][i];
   strcpy(optionfilegnuplot,optionfilefiname);          s2=s[mw[mi+1][i]][i];
   strcat(optionfilegnuplot,".gp.txt");          if( s2 > nlstate){ 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {            lli=log(out[s1][s2] - savm[s1][s2]);
     printf("Problem with file %s",optionfilegnuplot);          }else{
   }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
 #ifdef windows          ipmx +=1;
     fprintf(ficgp,"cd \"%s\" \n",pathc);          sw += weight[i];
 #endif          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 m=pow(2,cptcoveff);  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
          } /* end of wave */
  /* 1eme*/      } /* end of individual */
   for (cpt=1; cpt<= nlstate ; cpt ++) {    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
    for (k1=1; k1<= m ; k1 ++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 #ifdef windows        for(mi=1; mi<= wav[i]-1; mi++){
     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",ageminpar,fage,fileres,k1-1,k1-1);          for (ii=1;ii<=nlstate+ndeath;ii++)
 #endif            for (j=1;j<=nlstate+ndeath;j++){
 #ifdef unix              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 #endif            }
           for(d=0; d<dh[mi][i]; d++){
 for (i=1; i<= nlstate ; i ++) {            newm=savm;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for (kk=1; kk<=cptcovage;kk++) {
 }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);            }
     for (i=1; i<= nlstate ; i ++) {          
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   else fprintf(ficgp," \%%*lf (\%%*lf)");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            oldm=newm;
      for (i=1; i<= nlstate ; i ++) {          } /* end mult */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        
   else fprintf(ficgp," \%%*lf (\%%*lf)");          s1=s[mw[mi][i]][i];
 }            s2=s[mw[mi+1][i]][i];
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 #ifdef unix          ipmx +=1;
 fprintf(ficgp,"\nset ter gif small size 400,300");          sw += weight[i];
 #endif          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
    }        } /* end of wave */
   }      } /* end of individual */
   /*2 eme*/    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   for (k1=1; k1<= m ; k1 ++) {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
        return -l;
     for (i=1; i<= nlstate+1 ; i ++) {  }
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  /*************** log-likelihood *************/
       for (j=1; j<= nlstate+1 ; j ++) {  double funcone( double *x)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  {
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* Same as likeli but slower because of a lot of printf and if */
 }      int i, ii, j, k, mi, d, kk;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    double **out;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    double lli; /* Individual log likelihood */
       for (j=1; j<= nlstate+1 ; j ++) {    double llt;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int s1, s2;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    double bbh, survp;
 }      /*extern weight */
       fprintf(ficgp,"\" t\"\" w l 0,");    /* We are differentiating ll according to initial status */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       for (j=1; j<= nlstate+1 ; j ++) {    /*for(i=1;i<imx;i++) 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      printf(" %d\n",s[4][i]);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    */
 }      cov[1]=1.;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  
       else fprintf(ficgp,"\" t\"\" w l 0,");    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    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++){
   /*3eme*/        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
   for (k1=1; k1<= m ; k1 ++) {            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (cpt=1; cpt<= nlstate ; cpt ++) {            savm[ii][j]=(ii==j ? 1.0 : 0.0);
       k=2+nlstate*(cpt-1);          }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        for(d=0; d<dh[mi][i]; d++){
       for (i=1; i< nlstate ; i ++) {          newm=savm;
         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);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }          for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            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,
   /* CV preval stat */                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (k1=1; k1<= m ; k1 ++) {          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
     for (cpt=1; cpt<nlstate ; cpt ++) {          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
       k=3;          savm=oldm;
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          oldm=newm;
         } /* end mult */
       for (i=1; i< nlstate ; i ++)        
         fprintf(ficgp,"+$%d",k+i+1);        s1=s[mw[mi][i]][i];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        s2=s[mw[mi+1][i]][i];
              bbh=(double)bh[mi][i]/(double)stepm; 
       l=3+(nlstate+ndeath)*cpt;        /* bias is positive if real duration
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);         * is higher than the multiple of stepm and negative otherwise.
       for (i=1; i< nlstate ; i ++) {         */
         l=3+(nlstate+ndeath)*cpt;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         fprintf(ficgp,"+$%d",l+i+1);          lli=log(out[s1][s2] - savm[s1][s2]);
       }        } else if  (s2==-2) {
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            for (j=1,survp=0. ; j<=nlstate; j++) 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     }          lli= log(survp);
   }          }else if (mle==1){
            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   /* proba elementaires */        } else if(mle==2){
    for(i=1,jk=1; i <=nlstate; i++){          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(k=1; k <=(nlstate+ndeath); k++){        } else if(mle==3){  /* exponential inter-extrapolation */
       if (k != i) {          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 */
         for(j=1; j <=ncovmodel; j++){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
                  lli=log(out[s1][s2]); /* Original formula */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        } else{  /* mle=0 back to 1 */
           jk++;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           fprintf(ficgp,"\n");          /*lli=log(out[s1][s2]); */ /* Original formula */
         }        } /* End of if */
       }        ipmx +=1;
     }        sw += weight[i];
     }        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     for(jk=1; jk <=m; jk++) {        if(globpr){
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
    i=1;   %11.6f %11.6f %11.6f ", \
    for(k2=1; k2<=nlstate; k2++) {                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
      k3=i;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
      for(k=1; k<=(nlstate+ndeath); k++) {          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
        if (k != k2){            llt +=ll[k]*gipmx/gsw;
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
 ij=1;          }
         for(j=3; j <=ncovmodel; j++) {          fprintf(ficresilk," %10.6f\n", -llt);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        }
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      } /* end of wave */
             ij++;    } /* end of individual */
           }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           else    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         }    if(globpr==0){ /* First time we count the contributions and weights */
           fprintf(ficgp,")/(1");      gipmx=ipmx;
              gsw=sw;
         for(k1=1; k1 <=nlstate; k1++){      }
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    return -l;
 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]]]);  /*************** function likelione ***********/
             ij++;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
           }  {
           else    /* This routine should help understanding what is done with 
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);       the selection of individuals/waves and
           }       to check the exact contribution to the likelihood.
           fprintf(ficgp,")");       Plotting could be done.
         }     */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    int k;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  
         i=i+ncovmodel;    if(*globpri !=0){ /* Just counts and sums, no printings */
        }      strcpy(fileresilk,"ilk"); 
      }      strcat(fileresilk,fileres);
    }      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        printf("Problem with resultfile: %s\n", fileresilk);
    }        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
          }
   fclose(ficgp);      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");
 }  /* end gnuplot */      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       /*  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++) 
 /*************** Moving average **************/        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
   int i, cpt, cptcod;  
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    *fretone=(*funcone)(p);
       for (i=1; i<=nlstate;i++)    if(*globpri !=0){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      fclose(ficresilk);
           mobaverage[(int)agedeb][i][cptcod]=0.;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
          fflush(fichtm); 
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    } 
       for (i=1; i<=nlstate;i++){    return;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  }
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  
           }  /*********** Maximum Likelihood Estimation ***************/
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  
         }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       }  {
     }    int i,j, iter=0;
        double **xi;
 }    double fret;
     double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
 /************** Forecasting ******************/  
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){  #ifdef NLOPT
      int creturn;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    nlopt_opt opt;
   int *popage;    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double *lb;
   double *popeffectif,*popcount;    double minf; /* the minimum objective value, upon return */
   double ***p3mat;    double * p1; /* Shifted parameters from 0 instead of 1 */
   char fileresf[FILENAMELENGTH];    myfunc_data dinst, *d = &dinst;
   #endif
  agelim=AGESUP;  
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
     xi=matrix(1,npar,1,npar);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++)
          xi[i][j]=(i==j ? 1.0 : 0.0);
   strcpy(fileresf,"f");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   strcat(fileresf,fileres);    strcpy(filerespow,"pow"); 
   if((ficresf=fopen(fileresf,"w"))==NULL) {    strcat(filerespow,fileres);
     printf("Problem with forecast resultfile: %s\n", fileresf);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", filerespow);
   printf("Computing forecasting: result on file '%s' \n", fileresf);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
   if (mobilav==1) {      for(j=1;j<=nlstate+ndeath;j++)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    fprintf(ficrespow,"\n");
   }  #ifdef POWELL
     powell(p,xi,npar,ftol,&iter,&fret,func);
   stepsize=(int) (stepm+YEARM-1)/YEARM;  #endif
   if (stepm<=12) stepsize=1;  
    #ifdef NLOPT
   agelim=AGESUP;  #ifdef NEWUOA
      opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   hstepm=1;  #else
   hstepm=hstepm/stepm;    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   yp1=modf(dateintmean,&yp);  #endif
   anprojmean=yp;    lb=vector(0,npar-1);
   yp2=modf((yp1*12),&yp);    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
   mprojmean=yp;    nlopt_set_lower_bounds(opt, lb);
   yp1=modf((yp2*30.5),&yp);    nlopt_set_initial_step1(opt, 0.1);
   jprojmean=yp;    
   if(jprojmean==0) jprojmean=1;    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   if(mprojmean==0) jprojmean=1;    d->function = func;
      printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    nlopt_set_min_objective(opt, myfunc, d);
      nlopt_set_xtol_rel(opt, ftol);
   for(cptcov=1;cptcov<=i2;cptcov++){    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      printf("nlopt failed! %d\n",creturn); 
       k=k+1;    }
       fprintf(ficresf,"\n#******");    else {
       for(j=1;j<=cptcoveff;j++) {      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       }      iter=1; /* not equal */
       fprintf(ficresf,"******\n");    }
       fprintf(ficresf,"# StartingAge FinalAge");    nlopt_destroy(opt);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  #endif
          free_matrix(xi,1,npar,1,npar);
          fclose(ficrespow);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
         fprintf(ficresf,"\n");    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;  /**** Computes Hessian and covariance matrix ***/
            void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
           oldm=oldms;savm=savms;    double  **a,**y,*x,pd;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double **hess;
            int i, j;
           for (h=0; h<=nhstepm; h++){    int *indx;
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
             }    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
             for(j=1; j<=nlstate+ndeath;j++) {    void lubksb(double **a, int npar, int *indx, double b[]) ;
               kk1=0.;kk2=0;    void ludcmp(double **a, int npar, int *indx, double *d) ;
               for(i=1; i<=nlstate;i++) {                  double gompertz(double p[]);
                 if (mobilav==1)    hess=matrix(1,npar,1,npar);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {    printf("\nCalculation of the hessian matrix. Wait...\n");
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
                 }    for (i=1;i<=npar;i++){
                      printf("%d",i);fflush(stdout);
               }      fprintf(ficlog,"%d",i);fflush(ficlog);
               if (h==(int)(calagedate+12*cpt)){     
                 fprintf(ficresf," %.3f", kk1);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
                              
               }      /*  printf(" %f ",p[i]);
             }          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
           }    }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
         }    for (i=1;i<=npar;i++) {
       }      for (j=1;j<=npar;j++)  {
     }        if (j>i) { 
   }          printf(".%d%d",i,j);fflush(stdout);
                  fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
   fclose(ficresf);          hess[j][i]=hess[i][j];    
 }          /*printf(" %lf ",hess[i][j]);*/
 /************** Forecasting ******************/        }
 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;    printf("\n");
   int *popage;    fprintf(ficlog,"\n");
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   double ***p3mat,***tabpop,***tabpopprev;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   char filerespop[FILENAMELENGTH];    
     a=matrix(1,npar,1,npar);
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    y=matrix(1,npar,1,npar);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    x=vector(1,npar);
   agelim=AGESUP;    indx=ivector(1,npar);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    ludcmp(a,npar,indx,&pd);
    
      for (j=1;j<=npar;j++) {
   strcpy(filerespop,"pop");      for (i=1;i<=npar;i++) x[i]=0;
   strcat(filerespop,fileres);      x[j]=1;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      lubksb(a,npar,indx,x);
     printf("Problem with forecast resultfile: %s\n", filerespop);      for (i=1;i<=npar;i++){ 
   }        matcov[i][j]=x[i];
   printf("Computing forecasting: result on file '%s' \n", filerespop);      }
     }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
     printf("\n#Hessian matrix#\n");
   if (mobilav==1) {    fprintf(ficlog,"\n#Hessian matrix#\n");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for (i=1;i<=npar;i++) { 
     movingaverage(agedeb, fage, ageminpar, mobaverage);      for (j=1;j<=npar;j++) { 
   }        printf("%.3e ",hess[i][j]);
         fprintf(ficlog,"%.3e ",hess[i][j]);
   stepsize=(int) (stepm+YEARM-1)/YEARM;      }
   if (stepm<=12) stepsize=1;      printf("\n");
        fprintf(ficlog,"\n");
   agelim=AGESUP;    }
    
   hstepm=1;    /* Recompute Inverse */
   hstepm=hstepm/stepm;    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   if (popforecast==1) {    ludcmp(a,npar,indx,&pd);
     if((ficpop=fopen(popfile,"r"))==NULL) {  
       printf("Problem with population file : %s\n",popfile);exit(0);    /*  printf("\n#Hessian matrix recomputed#\n");
     }  
     popage=ivector(0,AGESUP);    for (j=1;j<=npar;j++) {
     popeffectif=vector(0,AGESUP);      for (i=1;i<=npar;i++) x[i]=0;
     popcount=vector(0,AGESUP);      x[j]=1;
          lubksb(a,npar,indx,x);
     i=1;        for (i=1;i<=npar;i++){ 
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        y[i][j]=x[i];
            printf("%.3e ",y[i][j]);
     imx=i;        fprintf(ficlog,"%.3e ",y[i][j]);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      }
   }      printf("\n");
       fprintf(ficlog,"\n");
   for(cptcov=1;cptcov<=i2;cptcov++){    }
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    */
       k=k+1;  
       fprintf(ficrespop,"\n#******");    free_matrix(a,1,npar,1,npar);
       for(j=1;j<=cptcoveff;j++) {    free_matrix(y,1,npar,1,npar);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_vector(x,1,npar);
       }    free_ivector(indx,1,npar);
       fprintf(ficrespop,"******\n");    free_matrix(hess,1,npar,1,npar);
       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++) {  /*************** hessian matrix ****************/
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
          {
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    int i;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    int l=1, lmax=20;
           nhstepm = nhstepm/hstepm;    double k1,k2;
              double p2[MAXPARM+1]; /* identical to x */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double res;
           oldm=oldms;savm=savms;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double fx;
            int k=0,kmax=10;
           for (h=0; h<=nhstepm; h++){    double l1;
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    fx=func(x);
             }    for (i=1;i<=npar;i++) p2[i]=x[i];
             for(j=1; j<=nlstate+ndeath;j++) {    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
               kk1=0.;kk2=0;      l1=pow(10,l);
               for(i=1; i<=nlstate;i++) {                    delts=delt;
                 if (mobilav==1)      for(k=1 ; k <kmax; k=k+1){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        delt = delta*(l1*k);
                 else {        p2[theta]=x[theta] +delt;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
                 }        p2[theta]=x[theta]-delt;
               }        k2=func(p2)-fx;
               if (h==(int)(calagedate+12*cpt)){        /*res= (k1-2.0*fx+k2)/delt/delt; */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
                   /*fprintf(ficrespop," %.3f", kk1);        
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  #ifdef DEBUGHESS
               }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
             }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
             for(i=1; i<=nlstate;i++){  #endif
               kk1=0.;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
                 for(j=1; j<=nlstate;j++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          k=kmax;
                 }        }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
             }          k=kmax; l=lmax*10;
         }
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);          delts=delt;
           }        }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
         }    }
       }    delti[theta]=delts;
      return res; 
   /******/    
   }
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    int i;
           nhstepm = nhstepm/hstepm;    int l=1, lmax=20;
              double k1,k2,k3,k4,res,fx;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double p2[MAXPARM+1];
           oldm=oldms;savm=savms;    int k;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           for (h=0; h<=nhstepm; h++){    fx=func(x);
             if (h==(int) (calagedate+YEARM*cpt)) {    for (k=1; k<=2; k++) {
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      for (i=1;i<=npar;i++) p2[i]=x[i];
             }      p2[thetai]=x[thetai]+delti[thetai]/k;
             for(j=1; j<=nlstate+ndeath;j++) {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
               kk1=0.;kk2=0;      k1=func(p2)-fx;
               for(i=1; i<=nlstate;i++) {                  
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];          p2[thetai]=x[thetai]+delti[thetai]/k;
               }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      k2=func(p2)-fx;
             }    
           }      p2[thetai]=x[thetai]-delti[thetai]/k;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         }      k3=func(p2)-fx;
       }    
    }      p2[thetai]=x[thetai]-delti[thetai]/k;
   }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k4=func(p2)-fx;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
   if (popforecast==1) {      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);
     free_ivector(popage,0,AGESUP);      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);
     free_vector(popeffectif,0,AGESUP);  #endif
     free_vector(popcount,0,AGESUP);    }
   }    return res;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  }
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   fclose(ficrespop);  /************** Inverse of matrix **************/
 }  void ludcmp(double **a, int n, int *indx, double *d) 
   { 
 /***********************************************/    int i,imax,j,k; 
 /**************** Main Program *****************/    double big,dum,sum,temp; 
 /***********************************************/    double *vv; 
    
 int main(int argc, char *argv[])    vv=vector(1,n); 
 {    *d=1.0; 
     for (i=1;i<=n;i++) { 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      big=0.0; 
   double agedeb, agefin,hf;      for (j=1;j<=n;j++) 
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   double fret;      vv[i]=1.0/big; 
   double **xi,tmp,delta;    } 
     for (j=1;j<=n;j++) { 
   double dum; /* Dummy variable */      for (i=1;i<j;i++) { 
   double ***p3mat;        sum=a[i][j]; 
   int *indx;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   char line[MAXLINE], linepar[MAXLINE];        a[i][j]=sum; 
   char title[MAXLINE];      } 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      big=0.0; 
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      for (i=j;i<=n;i++) { 
          sum=a[i][j]; 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
   char filerest[FILENAMELENGTH];        a[i][j]=sum; 
   char fileregp[FILENAMELENGTH];        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   char popfile[FILENAMELENGTH];          big=dum; 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          imax=i; 
   int firstobs=1, lastobs=10;        } 
   int sdeb, sfin; /* Status at beginning and end */      } 
   int c,  h , cpt,l;      if (j != imax) { 
   int ju,jl, mi;        for (k=1;k<=n;k++) { 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          dum=a[imax][k]; 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          a[imax][k]=a[j][k]; 
   int mobilav=0,popforecast=0;          a[j][k]=dum; 
   int hstepm, nhstepm;        } 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;        *d = -(*d); 
         vv[imax]=vv[j]; 
   double bage, fage, age, agelim, agebase;      } 
   double ftolpl=FTOL;      indx[j]=imax; 
   double **prlim;      if (a[j][j] == 0.0) a[j][j]=TINY; 
   double *severity;      if (j != n) { 
   double ***param; /* Matrix of parameters */        dum=1.0/(a[j][j]); 
   double  *p;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   double **matcov; /* Matrix of covariance */      } 
   double ***delti3; /* Scale */    } 
   double *delti; /* Scale */    free_vector(vv,1,n);  /* Doesn't work */
   double ***eij, ***vareij;  ;
   double **varpl; /* Variances of prevalence limits by age */  } 
   double *epj, vepp;  
   double kk1, kk2;  void lubksb(double **a, int n, int *indx, double b[]) 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  { 
      int i,ii=0,ip,j; 
     double sum; 
   char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";   
   char *alph[]={"a","a","b","c","d","e"}, str[4];    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
       sum=b[ip]; 
   char z[1]="c", occ;      b[ip]=b[i]; 
 #include <sys/time.h>      if (ii) 
 #include <time.h>        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      else if (sum) ii=i; 
        b[i]=sum; 
   /* long total_usecs;    } 
   struct timeval start_time, end_time;    for (i=n;i>=1;i--) { 
        sum=b[i]; 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   getcwd(pathcd, size);      b[i]=sum/a[i][i]; 
     } 
   printf("\n%s",version);  } 
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");  void pstamp(FILE *fichier)
     scanf("%s",pathtot);  {
   }    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   else{  }
     strcpy(pathtot,argv[1]);  
   }  /************ Frequencies ********************/
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
   /*cygwin_split_path(pathtot,path,optionfile);  {  /* Some frequencies */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    
   /* cutv(path,optionfile,pathtot,'\\');*/    int i, m, jk, j1, bool, z1,j;
     int first;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    double ***freq; /* Frequencies */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    double *pp, **prop;
   chdir(path);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   replace(pathc,path);    char fileresp[FILENAMELENGTH];
     
 /*-------- arguments in the command line --------*/    pp=vector(1,nlstate);
     prop=matrix(1,nlstate,iagemin,iagemax+3);
   strcpy(fileres,"r");    strcpy(fileresp,"p");
   strcat(fileres, optionfilefiname);    strcat(fileresp,fileres);
   strcat(fileres,".txt");    /* Other files have txt extension */    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
   /*---------arguments file --------*/      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    }
     printf("Problem with optionfile %s\n",optionfile);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     goto end;    j1=0;
   }    
     j=cptcoveff;
   strcpy(filereso,"o");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {    first=1;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
     /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
   /* Reads comments: lines beginning with '#' */    /*    j1++; */
   while((c=getc(ficpar))=='#' && c!= EOF){    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
     ungetc(c,ficpar);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     fgets(line, MAXLINE, ficpar);          scanf("%d", i);*/
     puts(line);        for (i=-5; i<=nlstate+ndeath; i++)  
     fputs(line,ficparo);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
   }            for(m=iagemin; m <= iagemax+3; m++)
   ungetc(c,ficpar);              freq[i][jk][m]=0;
         
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        for (i=1; i<=nlstate; i++)  
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);          for(m=iagemin; m <= iagemax+3; m++)
   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);            prop[i][m]=0;
 while((c=getc(ficpar))=='#' && c!= EOF){        
     ungetc(c,ficpar);        dateintsum=0;
     fgets(line, MAXLINE, ficpar);        k2cpt=0;
     puts(line);        for (i=1; i<=imx; i++) {
     fputs(line,ficparo);          bool=1;
   }          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
   ungetc(c,ficpar);            for (z1=1; z1<=cptcoveff; z1++)       
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
                      /* Tests if the value of each of the covariates of i is equal to filter j1 */
   covar=matrix(0,NCOVMAX,1,n);                bool=0;
   cptcovn=0;                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
                   j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
   ncovmodel=2+cptcovn;                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */              } 
            }
   /* Read guess parameters */   
   /* Reads comments: lines beginning with '#' */          if (bool==1){
   while((c=getc(ficpar))=='#' && c!= EOF){            for(m=firstpass; m<=lastpass; m++){
     ungetc(c,ficpar);              k2=anint[m][i]+(mint[m][i]/12.);
     fgets(line, MAXLINE, ficpar);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     puts(line);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fputs(line,ficparo);                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];
   ungetc(c,ficpar);                if (m<lastpass) {
                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     for(i=1; i <=nlstate; i++)                }
     for(j=1; j <=nlstate+ndeath-1; j++){                
       fscanf(ficpar,"%1d%1d",&i1,&j1);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       fprintf(ficparo,"%1d%1d",i1,j1);                  dateintsum=dateintsum+k2;
       printf("%1d%1d",i,j);                  k2cpt++;
       for(k=1; k<=ncovmodel;k++){                }
         fscanf(ficpar," %lf",&param[i][j][k]);                /*}*/
         printf(" %lf",param[i][j][k]);            }
         fprintf(ficparo," %lf",param[i][j][k]);          }
       }        } /* end i */
       fscanf(ficpar,"\n");         
       printf("\n");        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       fprintf(ficparo,"\n");        pstamp(ficresp);
     }        if  (cptcovn>0) {
            fprintf(ficresp, "\n#********** Variable "); 
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
   p=param[1][1];          fprintf(ficlog, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /* Reads comments: lines beginning with '#' */          fprintf(ficlog, "**********\n#");
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);        for(i=1; i<=nlstate;i++) 
     fgets(line, MAXLINE, ficpar);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     puts(line);        fprintf(ficresp, "\n");
     fputs(line,ficparo);        
   }        for(i=iagemin; i <= iagemax+3; i++){
   ungetc(c,ficpar);          if(i==iagemax+3){
             fprintf(ficlog,"Total");
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          }else{
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */            if(first==1){
   for(i=1; i <=nlstate; i++){              first=0;
     for(j=1; j <=nlstate+ndeath-1; j++){              printf("See log file for details...\n");
       fscanf(ficpar,"%1d%1d",&i1,&j1);            }
       printf("%1d%1d",i,j);            fprintf(ficlog,"Age %d", i);
       fprintf(ficparo,"%1d%1d",i1,j1);          }
       for(k=1; k<=ncovmodel;k++){          for(jk=1; jk <=nlstate ; jk++){
         fscanf(ficpar,"%le",&delti3[i][j][k]);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         printf(" %le",delti3[i][j][k]);              pp[jk] += freq[jk][m][i]; 
         fprintf(ficparo," %le",delti3[i][j][k]);          }
       }          for(jk=1; jk <=nlstate ; jk++){
       fscanf(ficpar,"\n");            for(m=-1, pos=0; m <=0 ; m++)
       printf("\n");              pos += freq[jk][m][i];
       fprintf(ficparo,"\n");            if(pp[jk]>=1.e-10){
     }              if(first==1){
   }                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   delti=delti3[1][1];              }
                fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   /* Reads comments: lines beginning with '#' */            }else{
   while((c=getc(ficpar))=='#' && c!= EOF){              if(first==1)
     ungetc(c,ficpar);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     fgets(line, MAXLINE, ficpar);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     puts(line);            }
     fputs(line,ficparo);          }
   }  
   ungetc(c,ficpar);          for(jk=1; jk <=nlstate ; jk++){
              for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   matcov=matrix(1,npar,1,npar);              pp[jk] += freq[jk][m][i];
   for(i=1; i <=npar; i++){          }       
     fscanf(ficpar,"%s",&str);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     printf("%s",str);            pos += pp[jk];
     fprintf(ficparo,"%s",str);            posprop += prop[jk][i];
     for(j=1; j <=i; j++){          }
       fscanf(ficpar," %le",&matcov[i][j]);          for(jk=1; jk <=nlstate ; jk++){
       printf(" %.5le",matcov[i][j]);            if(pos>=1.e-5){
       fprintf(ficparo," %.5le",matcov[i][j]);              if(first==1)
     }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     fscanf(ficpar,"\n");              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     printf("\n");            }else{
     fprintf(ficparo,"\n");              if(first==1)
   }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   for(i=1; i <=npar; i++)              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     for(j=i+1;j<=npar;j++)            }
       matcov[i][j]=matcov[j][i];            if( i <= iagemax){
                  if(pos>=1.e-5){
   printf("\n");                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     /*-------- Rewriting paramater file ----------*/              }
      strcpy(rfileres,"r");    /* "Rparameterfile */              else
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
      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;          for(jk=-1; jk <=nlstate+ndeath; jk++)
     }            for(m=-1; m <=nlstate+ndeath; m++)
     fprintf(ficres,"#%s\n",version);              if(freq[jk][m][i] !=0 ) {
                  if(first==1)
     /*-------- data file ----------*/                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     if((fic=fopen(datafile,"r"))==NULL)    {                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       printf("Problem with datafile: %s\n", datafile);goto end;              }
     }          if(i <= iagemax)
             fprintf(ficresp,"\n");
     n= lastobs;          if(first==1)
     severity = vector(1,maxwav);            printf("Others in log...\n");
     outcome=imatrix(1,maxwav+1,1,n);          fprintf(ficlog,"\n");
     num=ivector(1,n);        }
     moisnais=vector(1,n);        /*}*/
     annais=vector(1,n);    }
     moisdc=vector(1,n);    dateintmean=dateintsum/k2cpt; 
     andc=vector(1,n);   
     agedc=vector(1,n);    fclose(ficresp);
     cod=ivector(1,n);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     weight=vector(1,n);    free_vector(pp,1,nlstate);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     mint=matrix(1,maxwav,1,n);    /* End of Freq */
     anint=matrix(1,maxwav,1,n);  }
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);      /************ Prevalence ********************/
     tab=ivector(1,NCOVMAX);  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)
     ncodemax=ivector(1,8);  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     i=1;       in each health status at the date of interview (if between dateprev1 and dateprev2).
     while (fgets(line, MAXLINE, fic) != NULL)    {       We still use firstpass and lastpass as another selection.
       if ((i >= firstobs) && (i <=lastobs)) {    */
           
         for (j=maxwav;j>=1;j--){    int i, m, jk, j1, bool, z1,j;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  
           strcpy(line,stra);    double **prop;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double posprop; 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double  y2; /* in fractional years */
         }    int iagemin, iagemax;
            int first; /** to stop verbosity which is redirected to log file */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    iagemin= (int) agemin;
     iagemax= (int) agemax;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    /*pp=vector(1,nlstate);*/
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    j1=0;
         for (j=ncovcol;j>=1;j--){    
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    /*j=cptcoveff;*/
         }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         num[i]=atol(stra);    
            first=1;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/      /*for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;*/
         i=i+1;        
       }        for (i=1; i<=nlstate; i++)  
     }          for(m=iagemin; m <= iagemax+3; m++)
     /* printf("ii=%d", ij);            prop[i][m]=0.0;
        scanf("%d",i);*/       
   imx=i-1; /* Number of individuals */        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
   /* for (i=1; i<=imx; i++){          if  (cptcovn>0) {
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;            for (z1=1; z1<=cptcoveff; z1++) 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                bool=0;
     }*/          } 
            if (bool==1) { 
   /* for (i=1; i<=imx; i++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
      if (s[4][i]==9)  s[4][i]=-1;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
   /* Calculation of the number of parameter from char model*/                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   Tvar=ivector(1,15);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   Tprod=ivector(1,15);                  /*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]]);*/
   Tvaraff=ivector(1,15);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   Tvard=imatrix(1,15,1,2);                  prop[s[m][i]][iagemax+3] += weight[i]; 
   Tage=ivector(1,15);                      } 
                  }
   if (strlen(model) >1){            } /* end selection of waves */
     j=0, j1=0, k1=1, k2=1;          }
     j=nbocc(model,'+');        }
     j1=nbocc(model,'*');        for(i=iagemin; i <= iagemax+3; i++){  
     cptcovn=j+1;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     cptcovprod=j1;            posprop += prop[jk][i]; 
              } 
     strcpy(modelsav,model);          
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          for(jk=1; jk <=nlstate ; jk++){     
       printf("Error. Non available option model=%s ",model);            if( i <=  iagemax){ 
       goto end;              if(posprop>=1.e-5){ 
     }                probs[i][jk][j1]= prop[jk][i]/posprop;
                  } else{
     for(i=(j+1); i>=1;i--){                if(first==1){
       cutv(stra,strb,modelsav,'+');                  first=0;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                  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("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                }
       /*scanf("%d",i);*/              }
       if (strchr(strb,'*')) {            } 
         cutv(strd,strc,strb,'*');          }/* end jk */ 
         if (strcmp(strc,"age")==0) {        }/* end i */ 
           cptcovprod--;      /*} *//* end i1 */
           cutv(strb,stre,strd,'V');    } /* end j1 */
           Tvar[i]=atoi(stre);    
           cptcovage++;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
             Tage[cptcovage]=i;    /*free_vector(pp,1,nlstate);*/
             /*printf("stre=%s ", stre);*/    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
         }  }  /* End of prevalence */
         else if (strcmp(strd,"age")==0) {  
           cptcovprod--;  /************* Waves Concatenation ***************/
           cutv(strb,stre,strc,'V');  
           Tvar[i]=atoi(stre);  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)
           cptcovage++;  {
           Tage[cptcovage]=i;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         }       Death is a valid wave (if date is known).
         else {       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           cutv(strb,stre,strc,'V');       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           Tvar[i]=ncovcol+k1;       and mw[mi+1][i]. dh depends on stepm.
           cutv(strb,strc,strd,'V');       */
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);    int i, mi, m;
           Tvard[k1][2]=atoi(stre);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           Tvar[cptcovn+k2]=Tvard[k1][1];       double sum=0., jmean=0.;*/
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    int first;
           for (k=1; k<=lastobs;k++)    int j, k=0,jk, ju, jl;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    double sum=0.;
           k1++;    first=0;
           k2=k2+2;    jmin=100000;
         }    jmax=-1;
       }    jmean=0.;
       else {    for(i=1; i<=imx; i++){
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      mi=0;
        /*  scanf("%d",i);*/      m=firstpass;
       cutv(strd,strc,strb,'V');      while(s[m][i] <= nlstate){
       Tvar[i]=atoi(strc);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       }          mw[++mi][i]=m;
       strcpy(modelsav,stra);          if(m >=lastpass)
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          break;
         scanf("%d",i);*/        else
     }          m++;
 }      }/* end while */
        if (s[m][i] > nlstate){
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);        mi++;     /* Death is another wave */
   printf("cptcovprod=%d ", cptcovprod);        /* if(mi==0)  never been interviewed correctly before death */
   scanf("%d ",i);*/           /* Only death is a correct wave */
     fclose(fic);        mw[mi][i]=m;
       }
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/      wav[i]=mi;
       for(i=1;i<=n;i++) weight[i]=1.0;      if(mi==0){
     }        nbwarn++;
     /*-calculation of age at interview from date of interview and age at death -*/        if(first==0){
     agev=matrix(1,maxwav,1,imx);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           first=1;
     for (i=1; i<=imx; i++) {        }
       for(m=2; (m<= maxwav); m++) {        if(first==1){
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
          anint[m][i]=9999;        }
          s[m][i]=-1;      } /* end mi==0 */
        }    } /* End individuals */
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;  
       }    for(i=1; i<=imx; i++){
     }      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
     for (i=1; i<=imx; i++)  {          dh[mi][i]=1;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        else{
       for(m=1; (m<= maxwav); m++){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         if(s[m][i] >0){            if (agedc[i] < 2*AGESUP) {
           if (s[m][i] >= nlstate+1) {              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             if(agedc[i]>0)              if(j==0) j=1;  /* Survives at least one month after exam */
               if(moisdc[i]!=99 && andc[i]!=9999)              else if(j<0){
                 agev[m][i]=agedc[i];                nberr++;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
            else {                j=1; /* Temporary Dangerous patch */
               if (andc[i]!=9999){                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                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]);
               agev[m][i]=-1;                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               }              }
             }              k=k+1;
           }              if (j >= jmax){
           else if(s[m][i] !=9){ /* Should no more exist */                jmax=j;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);                ijmax=i;
             if(mint[m][i]==99 || anint[m][i]==9999)              }
               agev[m][i]=1;              if (j <= jmin){
             else if(agev[m][i] <agemin){                jmin=j;
               agemin=agev[m][i];                ijmin=i;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/              }
             }              sum=sum+j;
             else if(agev[m][i] >agemax){              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               agemax=agev[m][i];              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            }
             }          }
             /*agev[m][i]=anint[m][i]-annais[i];*/          else{
             /*   agev[m][i] = age[i]+2*m;*/            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           }  /*        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]); */
           else { /* =9 */  
             agev[m][i]=1;            k=k+1;
             s[m][i]=-1;            if (j >= jmax) {
           }              jmax=j;
         }              ijmax=i;
         else /*= 0 Unknown */            }
           agev[m][i]=1;            else if (j <= jmin){
       }              jmin=j;
                  ijmin=i;
     }            }
     for (i=1; i<=imx; i++)  {            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       for(m=1; (m<= maxwav); m++){            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
         if (s[m][i] > (nlstate+ndeath)) {            if(j<0){
           printf("Error: Wrong value in nlstate or ndeath\n");                nberr++;
           goto end;              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         }              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       }            }
     }            sum=sum+j;
           }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          jk= j/stepm;
           jl= j -jk*stepm;
     free_vector(severity,1,maxwav);          ju= j -(jk+1)*stepm;
     free_imatrix(outcome,1,maxwav+1,1,n);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     free_vector(moisnais,1,n);            if(jl==0){
     free_vector(annais,1,n);              dh[mi][i]=jk;
     /* free_matrix(mint,1,maxwav,1,n);              bh[mi][i]=0;
        free_matrix(anint,1,maxwav,1,n);*/            }else{ /* We want a negative bias in order to only have interpolation ie
     free_vector(moisdc,1,n);                    * to avoid the price of an extra matrix product in likelihood */
     free_vector(andc,1,n);              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
                }
     wav=ivector(1,imx);          }else{
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            if(jl <= -ju){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);              dh[mi][i]=jk;
                  bh[mi][i]=jl;       /* bias is positive if real duration
     /* Concatenates waves */                                   * is higher than the multiple of stepm and negative otherwise.
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);                                   */
             }
             else{
       Tcode=ivector(1,100);              dh[mi][i]=jk+1;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);              bh[mi][i]=ju;
       ncodemax[1]=1;            }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            if(dh[mi][i]==0){
                    dh[mi][i]=1; /* At least one step */
    codtab=imatrix(1,100,1,10);              bh[mi][i]=ju; /* At least one step */
    h=0;              /*  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);*/
    m=pow(2,cptcoveff);            }
            } /* end if mle */
    for(k=1;k<=cptcoveff; k++){        }
      for(i=1; i <=(m/pow(2,k));i++){      } /* end wave */
        for(j=1; j <= ncodemax[k]; j++){    }
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    jmean=sum/k;
            h++;    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    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);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/   }
          }  
        }  /*********** Tricode ****************************/
      }  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
    }  {
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
       codtab[1][2]=1;codtab[2][2]=2; */    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
    /* for(i=1; i <=m ;i++){     * Boring subroutine which should only output nbcode[Tvar[j]][k]
       for(k=1; k <=cptcovn; k++){     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);     * nbcode[Tvar[j]][1]= 
       }    */
       printf("\n");  
       }    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
       scanf("%d",i);*/    int modmaxcovj=0; /* Modality max of covariates j */
        int cptcode=0; /* Modality max of covariates j */
    /* Calculates basic frequencies. Computes observed prevalence at single age    int modmincovj=0; /* Modality min of covariates j */
        and prints on file fileres'p'. */  
   
        cptcoveff=0; 
       
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for (k=-1; k < maxncov; k++) Ndum[k]=0;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* Loop on covariates without age and products */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
            for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
     /* For Powell, parameters are in a vector p[] starting at p[1]                                 modality of this covariate Vj*/ 
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */                                      * If product of Vn*Vm, still boolean *:
                                       * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
     if(mle==1){                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
     }                                        modality of the nth covariate of individual i. */
            if (ij > modmaxcovj)
     /*--------- results files --------------*/          modmaxcovj=ij; 
     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);        else if (ij < modmincovj) 
            modmincovj=ij; 
         if ((ij < -1) && (ij > NCOVMAX)){
    jk=1;          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          exit(1);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        }else
    for(i=1,jk=1; i <=nlstate; i++){        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
      for(k=1; k <=(nlstate+ndeath); k++){        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
        if (k != i)        /*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
            printf("%d%d ",i,k);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
            fprintf(ficres,"%1d%1d ",i,k);           female is 1, then modmaxcovj=1.*/
            for(j=1; j <=ncovmodel; j++){      }
              printf("%f ",p[jk]);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
              fprintf(ficres,"%f ",p[jk]);      cptcode=modmaxcovj;
              jk++;      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
            }     /*for (i=0; i<=cptcode; i++) {*/
            printf("\n");      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
            fprintf(ficres,"\n");        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
          }        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
      }          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
    }        }
  if(mle==1){        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
     /* Computing hessian and covariance matrix */           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
     ftolhess=ftol; /* Usually correct */      } /* Ndum[-1] number of undefined modalities */
     hesscov(matcov, p, npar, delti, ftolhess, func);  
  }      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
     printf("# Scales (for hessian or gradient estimation)\n");      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
      for(i=1,jk=1; i <=nlstate; i++){         modmincovj=3; modmaxcovj = 7;
       for(j=1; j <=nlstate+ndeath; j++){         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
         if (j!=i) {         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(ficres,"%1d%1d",i,j);         variables V1_1 and V1_2.
           printf("%1d%1d",i,j);         nbcode[Tvar[j]][ij]=k;
           for(k=1; k<=ncovmodel;k++){         nbcode[Tvar[j]][1]=0;
             printf(" %.5e",delti[jk]);         nbcode[Tvar[j]][2]=1;
             fprintf(ficres," %.5e",delti[jk]);         nbcode[Tvar[j]][3]=2;
             jk++;      */
           }      ij=1; /* ij is similar to i but can jumps over null modalities */
           printf("\n");      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
           fprintf(ficres,"\n");        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
         }          /*recode from 0 */
       }          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
      }            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                                           k is a modality. If we have model=V1+V1*sex 
     k=1;                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");            ij++;
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");          }
     for(i=1;i<=npar;i++){          if (ij > ncodemax[j]) break; 
       /*  if (k>nlstate) k=1;        }  /* end of loop on */
       i1=(i-1)/(ncovmodel*nlstate)+1;      } /* end of loop on modality */ 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
       printf("%s%d%d",alph[k],i1,tab[i]);*/    
       fprintf(ficres,"%3d",i);   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
       printf("%3d",i);    
       for(j=1; j<=i;j++){    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
         fprintf(ficres," %.5e",matcov[i][j]);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
         printf(" %.5e",matcov[i][j]);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
       }     Ndum[ij]++; 
       fprintf(ficres,"\n");   } 
       printf("\n");  
       k++;   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]);*/
     while((c=getc(ficpar))=='#' && c!= EOF){     if((Ndum[i]!=0) && (i<=ncovcol)){
       ungetc(c,ficpar);       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
       fgets(line, MAXLINE, ficpar);       Tvaraff[ij]=i; /*For printing (unclear) */
       puts(line);       ij++;
       fputs(line,ficparo);     }else
     }         Tvaraff[ij]=0;
     ungetc(c,ficpar);   }
     estepm=0;   ij--;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);   cptcoveff=ij; /*Number of total covariates*/
     if (estepm==0 || estepm < stepm) estepm=stepm;  
     if (fage <= 2) {  }
       bage = ageminpar;  
       fage = agemaxpar;  
     }  /*********** Health Expectancies ****************/
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
     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);  {
      /* Health expectancies, no variances */
     while((c=getc(ficpar))=='#' && c!= EOF){    int i, j, nhstepm, hstepm, h, nstepm;
     ungetc(c,ficpar);    int nhstepma, nstepma; /* Decreasing with age */
     fgets(line, MAXLINE, ficpar);    double age, agelim, hf;
     puts(line);    double ***p3mat;
     fputs(line,ficparo);    double eip;
   }  
   ungetc(c,ficpar);    pstamp(ficreseij);
      fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    fprintf(ficreseij,"# Age");
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    for(i=1; i<=nlstate;i++){
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      for(j=1; j<=nlstate;j++){
              fprintf(ficreseij," e%1d%1d ",i,j);
   while((c=getc(ficpar))=='#' && c!= EOF){      }
     ungetc(c,ficpar);      fprintf(ficreseij," e%1d. ",i);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    fprintf(ficreseij,"\n");
     fputs(line,ficparo);  
   }    
   ungetc(c,ficpar);    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
     }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    else  hstepm=estepm;   
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
   fscanf(ficpar,"pop_based=%d\n",&popbased);     * if stepm=24 months pijx are given only every 2 years and by summing them
   fprintf(ficparo,"pop_based=%d\n",popbased);       * we are calculating an estimate of the Life Expectancy assuming a linear 
   fprintf(ficres,"pop_based=%d\n",popbased);       * progression in between and thus overestimating or underestimating according
       * to the curvature of the survival function. If, for the same date, we 
   while((c=getc(ficpar))=='#' && c!= EOF){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     ungetc(c,ficpar);     * to compare the new estimate of Life expectancy with the same linear 
     fgets(line, MAXLINE, ficpar);     * hypothesis. A more precise result, taking into account a more precise
     puts(line);     * curvature will be obtained if estepm is as small as stepm. */
     fputs(line,ficparo);  
   }    /* For example we decided to compute the life expectancy with the smallest unit */
   ungetc(c,ficpar);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
   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);       nstepm is the number of stepm from age to agelin. 
 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);       Look at hpijx to understand the reason of that which relies in memory size
 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);       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
 while((c=getc(ficpar))=='#' && c!= EOF){       means that if the survival funtion is printed only each two years of age and if
     ungetc(c,ficpar);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     fgets(line, MAXLINE, ficpar);       results. So we changed our mind and took the option of the best precision.
     puts(line);    */
     fputs(line,ficparo);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }  
   ungetc(c,ficpar);    agelim=AGESUP;
     /* If stepm=6 months */
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      
   /* nhstepm age range expressed in number of stepm */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 /*------------ gnuplot -------------*/    /* if (stepm >= YEARM) hstepm=1;*/
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 /*------------ free_vector  -------------*/  
  chdir(path);    for (age=bage; age<=fage; age ++){ 
        nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
  free_ivector(wav,1,imx);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      /* if (stepm >= YEARM) hstepm=1;*/
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);      /* If stepm=6 months */
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      /* Computed by stepm unit matrices, product of hstepma matrices, stored
  fclose(ficparo);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
  fclose(ficres);      
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
 /*--------- index.htm --------*/      
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);      
       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   /*--------------- Prevalence limit --------------*/      
        /* Computing expectancies */
   strcpy(filerespl,"pl");      for(i=1; i<=nlstate;i++)
   strcat(filerespl,fileres);        for(j=1; j<=nlstate;j++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   }            
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");          }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  
   fprintf(ficrespl,"\n");      fprintf(ficreseij,"%3.0f",age );
        for(i=1; i<=nlstate;i++){
   prlim=matrix(1,nlstate,1,nlstate);        eip=0;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1; j<=nlstate;j++){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          eip +=eij[i][j][(int)age];
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        fprintf(ficreseij,"%9.4f", eip );
   k=0;      }
   agebase=ageminpar;      fprintf(ficreseij,"\n");
   agelim=agemaxpar;      
   ftolpl=1.e-10;    }
   i1=cptcoveff;    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (cptcovn < 1){i1=1;}    printf("\n");
     fprintf(ficlog,"\n");
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  }
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  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[] )
         fprintf(ficrespl,"\n#******");  
         for(j=1;j<=cptcoveff;j++)  {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* Covariances of health expectancies eij and of total life expectancies according
         fprintf(ficrespl,"******\n");     to initial status i, ei. .
            */
         for (age=agebase; age<=agelim; age++){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    int nhstepma, nstepma; /* Decreasing with age */
           fprintf(ficrespl,"%.0f",age );    double age, agelim, hf;
           for(i=1; i<=nlstate;i++)    double ***p3matp, ***p3matm, ***varhe;
           fprintf(ficrespl," %.5f", prlim[i][i]);    double **dnewm,**doldm;
           fprintf(ficrespl,"\n");    double *xp, *xm;
         }    double **gp, **gm;
       }    double ***gradg, ***trgradg;
     }    int theta;
   fclose(ficrespl);  
     double eip, vip;
   /*------------- h Pij x at various ages ------------*/  
      varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    xp=vector(1,npar);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    xm=vector(1,npar);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    dnewm=matrix(1,nlstate*nlstate,1,npar);
   }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   printf("Computing pij: result on file '%s' \n", filerespij);    
      pstamp(ficresstdeij);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   /*if (stepm<=24) stepsize=2;*/    fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
   agelim=AGESUP;      for(j=1; j<=nlstate;j++)
   hstepm=stepsize*YEARM; /* Every year of age */        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      fprintf(ficresstdeij," e%1d. ",i);
      }
   k=0;    fprintf(ficresstdeij,"\n");
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    pstamp(ficrescveij);
       k=k+1;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
         fprintf(ficrespij,"\n#****** ");    fprintf(ficrescveij,"# Age");
         for(j=1;j<=cptcoveff;j++)    for(i=1; i<=nlstate;i++)
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(j=1; j<=nlstate;j++){
         fprintf(ficrespij,"******\n");        cptj= (j-1)*nlstate+i;
                for(i2=1; i2<=nlstate;i2++)
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          for(j2=1; j2<=nlstate;j2++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            cptj2= (j2-1)*nlstate+i2;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            if(cptj2 <= cptj)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           oldm=oldms;savm=savms;          }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        }
           fprintf(ficrespij,"# Age");    fprintf(ficrescveij,"\n");
           for(i=1; i<=nlstate;i++)    
             for(j=1; j<=nlstate+ndeath;j++)    if(estepm < stepm){
               fprintf(ficrespij," %1d-%1d",i,j);      printf ("Problem %d lower than %d\n",estepm, stepm);
           fprintf(ficrespij,"\n");    }
           for (h=0; h<=nhstepm; h++){    else  hstepm=estepm;   
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    /* We compute the life expectancy from trapezoids spaced every estepm months
             for(i=1; i<=nlstate;i++)     * This is mainly to measure the difference between two models: for example
               for(j=1; j<=nlstate+ndeath;j++)     * if stepm=24 months pijx are given only every 2 years and by summing them
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);     * we are calculating an estimate of the Life Expectancy assuming a linear 
             fprintf(ficrespij,"\n");     * progression in between and thus overestimating or underestimating according
           }     * to the curvature of the survival function. If, for the same date, we 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           fprintf(ficrespij,"\n");     * to compare the new estimate of Life expectancy with the same linear 
         }     * hypothesis. A more precise result, taking into account a more precise
     }     * curvature will be obtained if estepm is as small as stepm. */
   }  
     /* For example we decided to compute the life expectancy with the smallest unit */
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    /* 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 
   fclose(ficrespij);       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 */
   /*---------- Forecasting ------------------*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   if((stepm == 1) && (strcmp(model,".")==0)){       survival function given by stepm (the optimization length). Unfortunately it
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);       means that if the survival funtion is printed only each two years of age and if
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     free_matrix(mint,1,maxwav,1,n);       results. So we changed our mind and took the option of the best precision.
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    */
     free_vector(weight,1,n);}    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   else{  
     erreur=108;    /* If stepm=6 months */
     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);    /* 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 */ 
   /*---------- Health expectancies and variances ------------*/    /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   strcpy(filerest,"t");    
   strcat(filerest,fileres);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if((ficrest=fopen(filerest,"w"))==NULL) {    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   }    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
   strcpy(filerese,"e");    for (age=bage; age<=fage; age ++){ 
   strcat(filerese,fileres);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   if((ficreseij=fopen(filerese,"w"))==NULL) {      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      /* if (stepm >= YEARM) hstepm=1;*/
   }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
       /* If stepm=6 months */
  strcpy(fileresv,"v");      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   strcat(fileresv,fileres);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
   k=0;         decrease memory allocation */
   for(cptcov=1;cptcov<=i1;cptcov++){      for(theta=1; theta <=npar; theta++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(i=1; i<=npar; i++){ 
       k=k+1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficrest,"\n#****** ");          xm[i] = x[i] - (i==theta ?delti[theta]:0);
       for(j=1;j<=cptcoveff;j++)        }
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       fprintf(ficrest,"******\n");        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
       fprintf(ficreseij,"\n#****** ");        for(j=1; j<= nlstate; j++){
       for(j=1;j<=cptcoveff;j++)          for(i=1; i<=nlstate; i++){
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for(h=0; h<=nhstepm-1; h++){
       fprintf(ficreseij,"******\n");              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.;
       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");       
         for(ij=1; ij<= nlstate*nlstate; ij++)
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          for(h=0; h<=nhstepm-1; h++){
       oldm=oldms;savm=savms;            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);            }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      }/* End theta */
       oldm=oldms;savm=savms;      
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);      
          for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
            for(theta=1; theta <=npar; theta++)
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");            trgradg[h][j][theta]=gradg[h][theta][j];
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      
       fprintf(ficrest,"\n");  
        for(ij=1;ij<=nlstate*nlstate;ij++)
       epj=vector(1,nlstate+1);        for(ji=1;ji<=nlstate*nlstate;ji++)
       for(age=bage; age <=fage ;age++){          varhe[ij][ji][(int)age] =0.;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
         if (popbased==1) {       printf("%d|",(int)age);fflush(stdout);
           for(i=1; i<=nlstate;i++)       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
             prlim[i][i]=probs[(int)age][i][k];       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);
         fprintf(ficrest," %4.0f",age);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          for(ij=1;ij<=nlstate*nlstate;ij++)
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            for(ji=1;ji<=nlstate*nlstate;ji++)
             epj[j] += prlim[i][i]*eij[i][j][(int)age];              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
           }        }
           epj[nlstate+1] +=epj[j];      }
         }  
         for(i=1, vepp=0.;i <=nlstate;i++)      /* Computing expectancies */
           for(j=1;j <=nlstate;j++)      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
             vepp += vareij[i][j][(int)age];      for(i=1; i<=nlstate;i++)
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));        for(j=1; j<=nlstate;j++)
         for(j=1;j <=nlstate;j++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
         }            
         fprintf(ficrest,"\n");            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       }  
     }          }
   }  
       fprintf(ficresstdeij,"%3.0f",age );
   fclose(ficreseij);      for(i=1; i<=nlstate;i++){
   fclose(ficresvij);        eip=0.;
   fclose(ficrest);        vip=0.;
   fclose(ficpar);        for(j=1; j<=nlstate;j++){
   free_vector(epj,1,nlstate+1);          eip += eij[i][j][(int)age];
            for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   /*------- Variance limit prevalence------*/              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]) );
   strcpy(fileresvpl,"vpl");        }
   strcat(fileresvpl,fileres);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      fprintf(ficresstdeij,"\n");
     exit(0);  
   }      fprintf(ficrescveij,"%3.0f",age );
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   k=0;          cptj= (j-1)*nlstate+i;
   for(cptcov=1;cptcov<=i1;cptcov++){          for(i2=1; i2<=nlstate;i2++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            for(j2=1; j2<=nlstate;j2++){
       k=k+1;              cptj2= (j2-1)*nlstate+i2;
       fprintf(ficresvpl,"\n#****** ");              if(cptj2 <= cptj)
       for(j=1;j<=cptcoveff;j++)                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            }
       fprintf(ficresvpl,"******\n");        }
            fprintf(ficrescveij,"\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);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     }    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
  }    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   fclose(ficresvpl);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*---------- End : free ----------------*/    printf("\n");
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    fprintf(ficlog,"\n");
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    free_vector(xm,1,npar);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    free_vector(xp,1,npar);
      free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   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);  /************ 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[])
   free_matrix(matcov,1,npar,1,npar);  {
   free_vector(delti,1,npar);    /* Variance of health expectancies */
   free_matrix(agev,1,maxwav,1,imx);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    /* double **newm;*/
     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
   if(erreur >0)    
     printf("End of Imach with error or warning %d\n",erreur);    int movingaverage();
   else   printf("End of Imach\n");    double **dnewm,**doldm;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
   /* 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);*/    int k;
   /*printf("Total time was %d uSec.\n", total_usecs);*/    double *xp;
   /*------ End -----------*/    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
  end:    double *gpp, *gmp; /* for var p point j */
 #ifdef windows    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   /* chdir(pathcd);*/    double ***p3mat;
 #endif    double age,agelim, hf;
  /*system("wgnuplot graph.plt");*/    double ***mobaverage;
  /*system("../gp37mgw/wgnuplot graph.plt");*/    int theta;
  /*system("cd ../gp37mgw");*/    char digit[4];
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    char digitp[25];
  strcpy(plotcmd,GNUPLOTPROGRAM);  
  strcat(plotcmd," ");    char fileresprobmorprev[FILENAMELENGTH];
  strcat(plotcmd,optionfilegnuplot);  
  system(plotcmd);    if(popbased==1){
       if(mobilav!=0)
 #ifdef windows        strcpy(digitp,"-populbased-mobilav-");
   while (z[0] != 'q') {      else strcpy(digitp,"-populbased-nomobil-");
     /* chdir(path); */    }
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    else 
     scanf("%s",z);      strcpy(digitp,"-stablbased-");
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') system(optionfilehtm);    if (mobilav!=0) {
     else if (z[0] == 'g') system(plotcmd);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     else if (z[0] == 'q') exit(0);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 #endif        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"*/
      /* #include <gnu/libc-version.h> */ /* Only on gnu */
   #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(". ");fprintf(ficlog,". ");
      
   // 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.\n"); fprintf(ficlog," 32-bit.\n");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit.\n"); fprintf(ficlog," 64-bit.\n");/* 64-bit */
   #else
      printf(" wtf-bit.\n"); fprintf(ficlog," wtf-bit.\n");/* wtf */
   #endif
   
   /* struct utsname sysInfo;
   
      if (uname(&sysInfo) != -1) {
        printf(" %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog," %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
             */
   #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("GNU C version %d.\n", __GNUC_VERSION__);
      fprintf(ficlog, "GNU C version %d.\n", __GNUC_VERSION__);
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64())
              printf("The process is running under WOW64.\n");
      else
              printf("The process is not running under WOW64.\n");
   
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
     /* printf("GNU libc version: %s\n", gnu_get_libc_version()); */
   
    }
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     syscompilerinfo();
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.37  
changed lines
  Added in v.1.173


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