Diff for /imach/src/imach.c between versions 1.35 and 1.158

version 1.35, 2002/03/26 17:08:39 version 1.158, 2014/08/27 17:11:51
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.158  2014/08/27 17:11:51  brouard
      *** empty log message ***
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.157  2014/08/27 16:26:55  brouard
   first survey ("cross") where individuals from different ages are    Summary: Preparing windows Visual studio version
   interviewed on their health status or degree of disability (in the    Author: Brouard
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    In order to compile on Visual studio, time.h is now correct and time_t
   (if any) in individual health status.  Health expectancies are    and tm struct should be used. difftime should be used but sometimes I
   computed from the time spent in each health state according to a    just make the differences in raw time format (time(&now).
   model. More health states you consider, more time is necessary to reach the    Trying to suppress #ifdef LINUX
   Maximum Likelihood of the parameters involved in the model.  The    Add xdg-open for __linux in order to open default browser.
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.156  2014/08/25 20:10:10  brouard
   conditional to be observed in state i at the first wave. Therefore    *** empty log message ***
   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 1.155  2014/08/25 18:32:34  brouard
   complex model than "constant and age", you should modify the program    Summary: New compile, minor changes
   where the markup *Covariates have to be included here again* invites    Author: Brouard
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.154  2014/06/20 17:32:08  brouard
     Summary: Outputs now all graphs of convergence to period prevalence
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.153  2014/06/20 16:45:46  brouard
   identical for each individual. Also, if a individual missed an    Summary: If 3 live state, convergence to period prevalence on same graph
   intermediate interview, the information is lost, but taken into    Author: Brouard
   account using an interpolation or extrapolation.    
     Revision 1.152  2014/06/18 17:54:09  brouard
   hPijx is the probability to be observed in state i at age x+h    Summary: open browser, use gnuplot on same dir than imach if not found in the path
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.151  2014/06/18 16:43:30  brouard
   states. This elementary transition (by month or quarter trimester,    *** empty log message ***
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.150  2014/06/18 16:42:35  brouard
   and the contribution of each individual to the likelihood is simply    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
   hPijx.    Author: brouard
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.149  2014/06/18 15:51:14  brouard
   of the life expectancies. It also computes the prevalence limits.    Summary: Some fixes in parameter files errors
      Author: Nicolas Brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.148  2014/06/17 17:38:48  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: Nothing new
   from the European Union.    Author: Brouard
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Just a new packaging for OS/X version 0.98nS
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.147  2014/06/16 10:33:11  brouard
      *** empty log message ***
 #include <math.h>  
 #include <stdio.h>    Revision 1.146  2014/06/16 10:20:28  brouard
 #include <stdlib.h>    Summary: Merge
 #include <unistd.h>    Author: Brouard
   
 #define MAXLINE 256    Merge, before building revised version.
 #define GNUPLOTPROGRAM "wgnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.145  2014/06/10 21:23:15  brouard
 #define FILENAMELENGTH 80    Summary: Debugging with valgrind
 /*#define DEBUG*/    Author: Nicolas Brouard
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Lot of changes in order to output the results with some covariates
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    After the Edimburgh REVES conference 2014, it seems mandatory to
     improve the code.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    No more memory valgrind error but a lot has to be done in order to
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    continue the work of splitting the code into subroutines.
     Also, decodemodel has been improved. Tricode is still not
 #define NINTERVMAX 8    optimal. nbcode should be improved. Documentation has been added in
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    the source code.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.143  2014/01/26 09:45:38  brouard
 #define MAXN 20000    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define AGEBASE 40    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   
     Revision 1.142  2014/01/26 03:57:36  brouard
 int erreur; /* Error number */    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.141  2014/01/26 02:42:01  brouard
 int ndeath=1; /* Number of dead states */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.140  2011/09/02 10:37:54  brouard
     Summary: times.h is ok with mingw32 now.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.139  2010/06/14 07:50:17  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 int mle, weightopt;    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 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 1.138  2010/04/30 18:19:40  brouard
 double jmean; /* Mean space between 2 waves */    *** empty log message ***
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.137  2010/04/29 18:11:38  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    (Module): Checking covariates for more complex models
 FILE *ficgp,*ficresprob,*ficpop;    than V1+V2. A lot of change to be done. Unstable.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.136  2010/04/26 20:30:53  brouard
  FILE  *ficresvij;    (Module): merging some libgsl code. Fixing computation
   char fileresv[FILENAMELENGTH];    of likelione (using inter/intrapolation if mle = 0) in order to
  FILE  *ficresvpl;    get same likelihood as if mle=1.
   char fileresvpl[FILENAMELENGTH];    Some cleaning of code and comments added.
   
 #define NR_END 1    Revision 1.135  2009/10/29 15:33:14  brouard
 #define FREE_ARG char*    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define FTOL 1.0e-10  
     Revision 1.134  2009/10/29 13:18:53  brouard
 #define NRANSI    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define ITMAX 200  
     Revision 1.133  2009/07/06 10:21:25  brouard
 #define TOL 2.0e-4    just nforces
   
 #define CGOLD 0.3819660    Revision 1.132  2009/07/06 08:22:05  brouard
 #define ZEPS 1.0e-10    Many tings
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.131  2009/06/20 16:22:47  brouard
 #define GOLD 1.618034    Some dimensions resccaled
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
 static double maxarg1,maxarg2;    lot of cleaning with variables initialized to 0. Trying to make
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.129  2007/08/31 13:49:27  lievre
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 #define rint(a) floor(a+0.5)  
     Revision 1.128  2006/06/30 13:02:05  brouard
 static double sqrarg;    (Module): Clarifications on computing e.j
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 int imx;    imach-114 because nhstepm was no more computed in the age
 int stepm;    loop. Now we define nhstepma in the age loop.
 /* Stepm, step in month: minimum step interpolation*/    (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
 int m,nb;    and then all the health expectancies with variances or standard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    deviation (needs data from the Hessian matrices) which slows the
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    computation.
 double **pmmij, ***probs, ***mobaverage;    In the future we should be able to stop the program is only health
 double dateintmean=0;    expectancies and graph are needed without standard deviations.
   
 double *weight;    Revision 1.126  2006/04/28 17:23:28  brouard
 int **s; /* Status */    (Module): Yes the sum of survivors was wrong since
 double *agedc, **covar, idx;    imach-114 because nhstepm was no more computed in the age
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    loop. Now we define nhstepma in the age loop.
     Version 0.98h
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
 /**************** split *************************/    Forecasting file added.
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.124  2006/03/22 17:13:53  lievre
    char *s;                             /* pointer */    Parameters are printed with %lf instead of %f (more numbers after the comma).
    int  l1, l2;                         /* length counters */    The log-likelihood is printed in the log file
   
    l1 = strlen( path );                 /* length of path */    Revision 1.123  2006/03/20 10:52:43  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    * imach.c (Module): <title> changed, corresponds to .htm file
 #ifdef windows    name. <head> headers where missing.
    s = strrchr( path, '\\' );           /* find last / */  
 #else    * imach.c (Module): Weights can have a decimal point as for
    s = strrchr( path, '/' );            /* find last / */    English (a comma might work with a correct LC_NUMERIC environment,
 #endif    otherwise the weight is truncated).
    if ( s == NULL ) {                   /* no directory, so use current */    Modification of warning when the covariates values are not 0 or
 #if     defined(__bsd__)                /* get current working directory */    1.
       extern char       *getwd( );    Version 0.98g
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.122  2006/03/20 09:45:41  brouard
 #else    (Module): Weights can have a decimal point as for
       extern char       *getcwd( );    English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Modification of warning when the covariates values are not 0 or
 #endif    1.
          return( GLOCK_ERROR_GETCWD );    Version 0.98g
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.121  2006/03/16 17:45:01  lievre
    } else {                             /* strip direcotry from path */    * imach.c (Module): Comments concerning covariates added
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    * imach.c (Module): refinements in the computation of lli if
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    status=-2 in order to have more reliable computation if stepm is
       strcpy( name, s );                /* save file name */    not 1 month. Version 0.98f
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.120  2006/03/16 15:10:38  lievre
    }    (Module): refinements in the computation of lli if
    l1 = strlen( dirc );                 /* length of directory */    status=-2 in order to have more reliable computation if stepm is
 #ifdef windows    not 1 month. Version 0.98f
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Revision 1.119  2006/03/15 17:42:26  brouard
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    (Module): Bug if status = -2, the loglikelihood was
 #endif    computed as likelihood omitting the logarithm. Version O.98e
    s = strrchr( name, '.' );            /* find last / */  
    s++;    Revision 1.118  2006/03/14 18:20:07  brouard
    strcpy(ext,s);                       /* save extension */    (Module): varevsij Comments added explaining the second
    l1= strlen( name);    table of variances if popbased=1 .
    l2= strlen( s)+1;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    strncpy( finame, name, l1-l2);    (Module): Function pstamp added
    finame[l1-l2]= 0;    (Module): Version 0.98d
    return( 0 );                         /* we're done */  
 }    Revision 1.117  2006/03/14 17:16:22  brouard
     (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
 /******************************************/    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 void replace(char *s, char*t)    (Module): Version 0.98d
 {  
   int i;    Revision 1.116  2006/03/06 10:29:27  brouard
   int lg=20;    (Module): Variance-covariance wrong links and
   i=0;    varian-covariance of ej. is needed (Saito).
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.115  2006/02/27 12:17:45  brouard
     (s[i] = t[i]);    (Module): One freematrix added in mlikeli! 0.98c
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.114  2006/02/26 12:57:58  brouard
 }    (Module): Some improvements in processing parameter
     filename with strsep.
 int nbocc(char *s, char occ)  
 {    Revision 1.113  2006/02/24 14:20:24  brouard
   int i,j=0;    (Module): Memory leaks checks with valgrind and:
   int lg=20;    datafile was not closed, some imatrix were not freed and on matrix
   i=0;    allocation too.
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.112  2006/01/30 09:55:26  brouard
   if  (s[i] == occ ) j++;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   }  
   return j;    Revision 1.111  2006/01/25 20:38:18  brouard
 }    (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
 void cutv(char *u,char *v, char*t, char occ)    can be a simple dot '.'.
 {  
   int i,lg,j,p=0;    Revision 1.110  2006/01/25 00:51:50  brouard
   i=0;    (Module): Lots of cleaning and bugs added (Gompertz)
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Revision 1.109  2006/01/24 19:37:15  brouard
   }    (Module): Comments (lines starting with a #) are allowed in data.
   
   lg=strlen(t);    Revision 1.108  2006/01/19 18:05:42  lievre
   for(j=0; j<p; j++) {    Gnuplot problem appeared...
     (u[j] = t[j]);    To be fixed
   }  
      u[p]='\0';    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Revision 1.106  2006/01/19 13:24:36  brouard
   }    Some cleaning and links added in html output
 }  
     Revision 1.105  2006/01/05 20:23:19  lievre
 /********************** nrerror ********************/    *** empty log message ***
   
 void nrerror(char error_text[])    Revision 1.104  2005/09/30 16:11:43  lievre
 {    (Module): sump fixed, loop imx fixed, and simplifications.
   fprintf(stderr,"ERREUR ...\n");    (Module): If the status is missing at the last wave but we know
   fprintf(stderr,"%s\n",error_text);    that the person is alive, then we can code his/her status as -2
   exit(1);    (instead of missing=-1 in earlier versions) and his/her
 }    contributions to the likelihood is 1 - Prob of dying from last
 /*********************** vector *******************/    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 double *vector(int nl, int nh)    the healthy state at last known wave). Version is 0.98
 {  
   double *v;    Revision 1.103  2005/09/30 15:54:49  lievre
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    (Module): sump fixed, loop imx fixed, and simplifications.
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.102  2004/09/15 17:31:30  brouard
 }    Add the possibility to read data file including tab characters.
   
 /************************ free vector ******************/    Revision 1.101  2004/09/15 10:38:38  brouard
 void free_vector(double*v, int nl, int nh)    Fix on curr_time
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.100  2004/07/12 18:29:06  brouard
 }    Add version for Mac OS X. Just define UNIX in Makefile
   
 /************************ivector *******************************/    Revision 1.99  2004/06/05 08:57:40  brouard
 int *ivector(long nl,long nh)    *** empty log message ***
 {  
   int *v;    Revision 1.98  2004/05/16 15:05:56  brouard
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    New version 0.97 . First attempt to estimate force of mortality
   if (!v) nrerror("allocation failure in ivector");    directly from the data i.e. without the need of knowing the health
   return v-nl+NR_END;    state at each age, but using a Gompertz model: log u =a + b*age .
 }    This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
 /******************free ivector **************************/    cross-longitudinal survey is different from the mortality estimated
 void free_ivector(int *v, long nl, long nh)    from other sources like vital statistic data.
 {  
   free((FREE_ARG)(v+nl-NR_END));    The same imach parameter file can be used but the option for mle should be -3.
 }  
     Agnès, who wrote this part of the code, tried to keep most of the
 /******************* imatrix *******************************/    former routines in order to include the new code within the former code.
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    The output is very simple: only an estimate of the intercept and of
 {    the slope with 95% confident intervals.
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    Current limitations:
      A) Even if you enter covariates, i.e. with the
   /* allocate pointers to rows */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    B) There is no computation of Life Expectancy nor Life Table.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.97  2004/02/20 13:25:42  lievre
   m -= nrl;    Version 0.96d. Population forecasting command line is (temporarily)
      suppressed.
    
   /* allocate rows and set pointers to them */    Revision 1.96  2003/07/15 15:38:55  brouard
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    rewritten within the same printf. Workaround: many printfs.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.95  2003/07/08 07:54:34  brouard
      * imach.c (Repository):
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    (Repository): Using imachwizard code to output a more meaningful covariance
      matrix (cov(a12,c31) instead of numbers.
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.94  2003/06/27 13:00:02  brouard
 }    Just cleaning
   
 /****************** free_imatrix *************************/    Revision 1.93  2003/06/25 16:33:55  brouard
 void free_imatrix(m,nrl,nrh,ncl,nch)    (Module): On windows (cygwin) function asctime_r doesn't
       int **m;    exist so I changed back to asctime which exists.
       long nch,ncl,nrh,nrl;    (Module): Version 0.96b
      /* free an int matrix allocated by imatrix() */  
 {    Revision 1.92  2003/06/25 16:30:45  brouard
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    (Module): On windows (cygwin) function asctime_r doesn't
   free((FREE_ARG) (m+nrl-NR_END));    exist so I changed back to asctime which exists.
 }  
     Revision 1.91  2003/06/25 15:30:29  brouard
 /******************* matrix *******************************/    * imach.c (Repository): Duplicated warning errors corrected.
 double **matrix(long nrl, long nrh, long ncl, long nch)    (Repository): Elapsed time after each iteration is now output. It
 {    helps to forecast when convergence will be reached. Elapsed time
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    is stamped in powell.  We created a new html file for the graphs
   double **m;    concerning matrix of covariance. It has extension -cov.htm.
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.90  2003/06/24 12:34:15  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Some bugs corrected for windows. Also, when
   m += NR_END;    mle=-1 a template is output in file "or"mypar.txt with the design
   m -= nrl;    of the covariance matrix to be input.
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Revision 1.89  2003/06/24 12:30:52  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): Some bugs corrected for windows. Also, when
   m[nrl] += NR_END;    mle=-1 a template is output in file "or"mypar.txt with the design
   m[nrl] -= ncl;    of the covariance matrix to be input.
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.88  2003/06/23 17:54:56  brouard
   return m;    * 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.
 }  
     Revision 1.87  2003/06/18 12:26:01  brouard
 /*************************free matrix ************************/    Version 0.96
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {    Revision 1.86  2003/06/17 20:04:08  brouard
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    (Module): Change position of html and gnuplot routines and added
   free((FREE_ARG)(m+nrl-NR_END));    routine fileappend.
 }  
     Revision 1.85  2003/06/17 13:12:43  brouard
 /******************* ma3x *******************************/    * imach.c (Repository): Check when date of death was earlier that
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    current date of interview. It may happen when the death was just
 {    prior to the death. In this case, dh was negative and likelihood
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    was wrong (infinity). We still send an "Error" but patch by
   double ***m;    assuming that the date of death was just one stepm after the
     interview.
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    (Repository): Because some people have very long ID (first column)
   if (!m) nrerror("allocation failure 1 in matrix()");    we changed int to long in num[] and we added a new lvector for
   m += NR_END;    memory allocation. But we also truncated to 8 characters (left
   m -= nrl;    truncation)
     (Repository): No more line truncation errors.
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.84  2003/06/13 21:44:43  brouard
   m[nrl] += NR_END;    * imach.c (Repository): Replace "freqsummary" at a correct
   m[nrl] -= ncl;    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    Revision 1.83  2003/06/10 13:39:11  lievre
   m[nrl][ncl] += NR_END;    *** empty log message ***
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)    Revision 1.82  2003/06/05 15:57:20  brouard
     m[nrl][j]=m[nrl][j-1]+nlay;    Add log in  imach.c and  fullversion number is now printed.
    
   for (i=nrl+1; i<=nrh; i++) {  */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  /*
     for (j=ncl+1; j<=nch; j++)     Interpolated Markov Chain
       m[i][j]=m[i][j-1]+nlay;  
   }    Short summary of the programme:
   return m;    
 }    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 /*************************free ma3x ************************/    first survey ("cross") where individuals from different ages are
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    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
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    second wave of interviews ("longitudinal") which measure each change
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    (if any) in individual health status.  Health expectancies are
   free((FREE_ARG)(m+nrl-NR_END));    computed from the time spent in each health state according to a
 }    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
 /***************** f1dim *************************/    simplest model is the multinomial logistic model where pij is the
 extern int ncom;    probability to be observed in state j at the second wave
 extern double *pcom,*xicom;    conditional to be observed in state i at the first wave. Therefore
 extern double (*nrfunc)(double []);    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
 double f1dim(double x)    complex model than "constant and age", you should modify the program
 {    where the markup *Covariates have to be included here again* invites
   int j;    you to do it.  More covariates you add, slower the
   double f;    convergence.
   double *xt;  
      The advantage of this computer programme, compared to a simple
   xt=vector(1,ncom);    multinomial logistic model, is clear when the delay between waves is not
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    identical for each individual. Also, if a individual missed an
   f=(*nrfunc)(xt);    intermediate interview, the information is lost, but taken into
   free_vector(xt,1,ncom);    account using an interpolation or extrapolation.  
   return f;  
 }    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
 /*****************brent *************************/    split into an exact number (nh*stepm) of unobserved intermediate
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    states. This elementary transition (by month, quarter,
 {    semester or year) is modelled as a multinomial logistic.  The hPx
   int iter;    matrix is simply the matrix product of nh*stepm elementary matrices
   double a,b,d,etemp;    and the contribution of each individual to the likelihood is simply
   double fu,fv,fw,fx;    hPijx.
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;    Also this programme outputs the covariance matrix of the parameters but also
   double e=0.0;    of the life expectancies. It also computes the period (stable) prevalence. 
      
   a=(ax < cx ? ax : cx);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   b=(ax > cx ? ax : cx);             Institut national d'études démographiques, Paris.
   x=w=v=bx;    This software have been partly granted by Euro-REVES, a concerted action
   fw=fv=fx=(*f)(x);    from the European Union.
   for (iter=1;iter<=ITMAX;iter++) {    It is copyrighted identically to a GNU software product, ie programme and
     xm=0.5*(a+b);    software can be distributed freely for non commercial use. Latest version
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    can be accessed at http://euroreves.ined.fr/imach .
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #ifdef DEBUG    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    **********************************************************************/
 #endif  /*
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    main
       *xmin=x;    read parameterfile
       return fx;    read datafile
     }    concatwav
     ftemp=fu;    freqsummary
     if (fabs(e) > tol1) {    if (mle >= 1)
       r=(x-w)*(fx-fv);      mlikeli
       q=(x-v)*(fx-fw);    print results files
       p=(x-v)*q-(x-w)*r;    if mle==1 
       q=2.0*(q-r);       computes hessian
       if (q > 0.0) p = -p;    read end of parameter file: agemin, agemax, bage, fage, estepm
       q=fabs(q);        begin-prev-date,...
       etemp=e;    open gnuplot file
       e=d;    open html file
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
         d=CGOLD*(e=(x >= xm ? a-x : b-x));     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
       else {                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
         d=p/q;      freexexit2 possible for memory heap.
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)    h Pij x                         | pij_nom  ficrestpij
           d=SIGN(tol1,xm-x);     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
       }         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
     } else {         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
     fu=(*f)(u);    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
     if (fu <= fx) {     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
       if (u >= x) a=x; else b=x;     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)    forecasting if prevfcast==1 prevforecast call prevalence()
         } else {    health expectancies
           if (u < x) a=u; else b=u;    Variance-covariance of DFLE
           if (fu <= fw || w == x) {    prevalence()
             v=w;     movingaverage()
             w=u;    varevsij() 
             fv=fw;    if popbased==1 varevsij(,popbased)
             fw=fu;    total life expectancies
           } else if (fu <= fv || v == x || v == w) {    Variance of period (stable) prevalence
             v=u;   end
             fv=fu;  */
           }  
         }  
   }  
   nrerror("Too many iterations in brent");   
   *xmin=x;  #include <math.h>
   return fx;  #include <stdio.h>
 }  #include <stdlib.h>
   #include <string.h>
 /****************** mnbrak ***********************/  #include <unistd.h>
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #include <limits.h>
             double (*func)(double))  #include <sys/types.h>
 {  #include <sys/stat.h>
   double ulim,u,r,q, dum;  #include <errno.h>
   double fu;  extern int errno;
    
   *fa=(*func)(*ax);  /* #ifdef LINUX */
   *fb=(*func)(*bx);  /* #include <time.h> */
   if (*fb > *fa) {  /* #include "timeval.h" */
     SHFT(dum,*ax,*bx,dum)  /* #else */
       SHFT(dum,*fb,*fa,dum)  /* #include <sys/time.h> */
       }  /* #endif */
   *cx=(*bx)+GOLD*(*bx-*ax);  
   *fc=(*func)(*cx);  #include <time.h>
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  #ifdef GSL
     q=(*bx-*cx)*(*fb-*fa);  #include <gsl/gsl_errno.h>
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #include <gsl/gsl_multimin.h>
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #endif
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {  /* #include <libintl.h> */
       fu=(*func)(u);  /* #define _(String) gettext (String) */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define GNUPLOTPROGRAM "gnuplot"
           SHFT(*fb,*fc,fu,(*func)(u))  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
           }  #define FILENAMELENGTH 132
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       fu=(*func)(u);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
       fu=(*func)(u);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
     }  
     SHFT(*ax,*bx,*cx,u)  #define NINTERVMAX 8
       SHFT(*fa,*fb,*fc,fu)  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
       }  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 }  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
   #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
 /*************** linmin ************************/  #define MAXN 20000
   #define YEARM 12. /**< Number of months per year */
 int ncom;  #define AGESUP 130
 double *pcom,*xicom;  #define AGEBASE 40
 double (*nrfunc)(double []);  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
    #ifdef _WIN32
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  #define DIRSEPARATOR '\\'
 {  #define CHARSEPARATOR "\\"
   double brent(double ax, double bx, double cx,  #define ODIRSEPARATOR '/'
                double (*f)(double), double tol, double *xmin);  #else
   double f1dim(double x);  #define DIRSEPARATOR '/'
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  #define CHARSEPARATOR "/"
               double *fc, double (*func)(double));  #define ODIRSEPARATOR '\\'
   int j;  #endif
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  /* $Id$ */
    /* $State$ */
   ncom=n;  
   pcom=vector(1,n);  char version[]="Imach version 0.98nX, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
   xicom=vector(1,n);  char fullversion[]="$Revision$ $Date$"; 
   nrfunc=func;  char strstart[80];
   for (j=1;j<=n;j++) {  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
     pcom[j]=p[j];  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     xicom[j]=xi[j];  int nvar=0, nforce=0; /* Number of variables, number of forces */
   }  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   ax=0.0;  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   xx=1.0;  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
 #ifdef DEBUG  int cptcovprodnoage=0; /**< Number of covariate products without age */   
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  int cptcoveff=0; /* Total number of covariates to vary for printing results */
 #endif  int cptcov=0; /* Working variable */
   for (j=1;j<=n;j++) {  int npar=NPARMAX;
     xi[j] *= xmin;  int nlstate=2; /* Number of live states */
     p[j] += xi[j];  int ndeath=1; /* Number of dead states */
   }  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   free_vector(xicom,1,n);  int popbased=0;
   free_vector(pcom,1,n);  
 }  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav=0; /* Maxim number of waves */
 /*************** powell ************************/  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
             double (*func)(double []))  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
 {                     to the likelihood and the sum of weights (done by funcone)*/
   void linmin(double p[], double xi[], int n, double *fret,  int mle=1, weightopt=0;
               double (*func)(double []));  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int i,ibig,j;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   double del,t,*pt,*ptt,*xit;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   double fp,fptt;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double *xits;  double jmean=1; /* Mean space between 2 waves */
   pt=vector(1,n);  double **matprod2(); /* test */
   ptt=vector(1,n);  double **oldm, **newm, **savm; /* Working pointers to matrices */
   xit=vector(1,n);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   xits=vector(1,n);  /*FILE *fic ; */ /* Used in readdata only */
   *fret=(*func)(p);  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   for (j=1;j<=n;j++) pt[j]=p[j];  FILE *ficlog, *ficrespow;
   for (*iter=1;;++(*iter)) {  int globpr=0; /* Global variable for printing or not */
     fp=(*fret);  double fretone; /* Only one call to likelihood */
     ibig=0;  long ipmx=0; /* Number of contributions */
     del=0.0;  double sw; /* Sum of weights */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  char filerespow[FILENAMELENGTH];
     for (i=1;i<=n;i++)  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       printf(" %d %.12f",i, p[i]);  FILE *ficresilk;
     printf("\n");  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     for (i=1;i<=n;i++) {  FILE *ficresprobmorprev;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  FILE *fichtm, *fichtmcov; /* Html File */
       fptt=(*fret);  FILE *ficreseij;
 #ifdef DEBUG  char filerese[FILENAMELENGTH];
       printf("fret=%lf \n",*fret);  FILE *ficresstdeij;
 #endif  char fileresstde[FILENAMELENGTH];
       printf("%d",i);fflush(stdout);  FILE *ficrescveij;
       linmin(p,xit,n,fret,func);  char filerescve[FILENAMELENGTH];
       if (fabs(fptt-(*fret)) > del) {  FILE  *ficresvij;
         del=fabs(fptt-(*fret));  char fileresv[FILENAMELENGTH];
         ibig=i;  FILE  *ficresvpl;
       }  char fileresvpl[FILENAMELENGTH];
 #ifdef DEBUG  char title[MAXLINE];
       printf("%d %.12e",i,(*fret));  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       for (j=1;j<=n;j++) {  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
         printf(" x(%d)=%.12e",j,xit[j]);  char command[FILENAMELENGTH];
       }  int  outcmd=0;
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       printf("\n");  
 #endif  char filelog[FILENAMELENGTH]; /* Log file */
     }  char filerest[FILENAMELENGTH];
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  char fileregp[FILENAMELENGTH];
 #ifdef DEBUG  char popfile[FILENAMELENGTH];
       int k[2],l;  
       k[0]=1;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
       for (j=1;j<=n;j++)  /* struct timezone tzp; */
         printf(" %.12e",p[j]);  /* extern int gettimeofday(); */
       printf("\n");  struct tm tml, *gmtime(), *localtime();
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  extern time_t time();
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  struct tm start_time, end_time, curr_time, last_time, forecast_time;
         }  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  struct tm tm;
       }  
 #endif  char strcurr[80], strfor[80];
   
   char *endptr;
       free_vector(xit,1,n);  long lval;
       free_vector(xits,1,n);  double dval;
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);  #define NR_END 1
       return;  #define FREE_ARG char*
     }  #define FTOL 1.0e-10
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {  #define NRANSI 
       ptt[j]=2.0*p[j]-pt[j];  #define ITMAX 200 
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  #define TOL 2.0e-4 
     }  
     fptt=(*func)(ptt);  #define CGOLD 0.3819660 
     if (fptt < fp) {  #define ZEPS 1.0e-10 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  #define GOLD 1.618034 
         for (j=1;j<=n;j++) {  #define GLIMIT 100.0 
           xi[j][ibig]=xi[j][n];  #define TINY 1.0e-20 
           xi[j][n]=xit[j];  
         }  static double maxarg1,maxarg2;
 #ifdef DEBUG  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
         for(j=1;j<=n;j++)    
           printf(" %.12e",xit[j]);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
         printf("\n");  #define rint(a) floor(a+0.5)
 #endif  
       }  static double sqrarg;
     }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 }  int agegomp= AGEGOMP;
   
 /**** Prevalence limit ****************/  int imx; 
   int stepm=1;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  /* Stepm, step in month: minimum step interpolation*/
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  int estepm;
      matrix by transitions matrix until convergence is reached */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
   int i, ii,j,k;  int m,nb;
   double min, max, maxmin, maxmax,sumnew=0.;  long *num;
   double **matprod2();  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double **out, cov[NCOVMAX], **pmij();  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **newm;  double **pmmij, ***probs;
   double agefin, delaymax=50 ; /* Max number of years to converge */  double *ageexmed,*agecens;
   double dateintmean=0;
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  double *weight;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  int **s; /* Status */
     }  double *agedc;
   double  **covar; /**< covar[j,i], value of jth covariate for individual i,
    cov[1]=1.;                    * covar=matrix(0,NCOVMAX,1,n); 
                      * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  double  idx; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
     newm=savm;  int *Ndum; /** Freq of modality (tricode */
     /* Covariates have to be included here again */  int **codtab; /**< codtab=imatrix(1,100,1,10); */
      cov[2]=agefin;  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
    double *lsurv, *lpop, *tpop;
       for (k=1; k<=cptcovn;k++) {  
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
         /*      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]]);*/  double ftolhess; /**< Tolerance for computing hessian */
       }  
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /**************** split *************************/
       for (k=1; k<=cptcovprod;k++)  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  {
     /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    */ 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    char  *ss;                            /* pointer */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    int   l1, l2;                         /* length counters */
   
     savm=oldm;    l1 = strlen(path );                   /* length of path */
     oldm=newm;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     maxmax=0.;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     for(j=1;j<=nlstate;j++){    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       min=1.;      strcpy( name, path );               /* we got the fullname name because no directory */
       max=0.;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       for(i=1; i<=nlstate; i++) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
         sumnew=0;      /* get current working directory */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      /*    extern  char* getcwd ( char *buf , int len);*/
         prlim[i][j]= newm[i][j]/(1-sumnew);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         max=FMAX(max,prlim[i][j]);        return( GLOCK_ERROR_GETCWD );
         min=FMIN(min,prlim[i][j]);      }
       }      /* got dirc from getcwd*/
       maxmin=max-min;      printf(" DIRC = %s \n",dirc);
       maxmax=FMAX(maxmax,maxmin);    } else {                              /* strip direcotry from path */
     }      ss++;                               /* after this, the filename */
     if(maxmax < ftolpl){      l2 = strlen( ss );                  /* length of filename */
       return prlim;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     }      strcpy( name, ss );         /* save file name */
   }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 }      dirc[l1-l2] = 0;                    /* add zero */
       printf(" DIRC2 = %s \n",dirc);
 /*************** transition probabilities ***************/    }
     /* We add a separator at the end of dirc if not exists */
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    l1 = strlen( dirc );                  /* length of directory */
 {    if( dirc[l1-1] != DIRSEPARATOR ){
   double s1, s2;      dirc[l1] =  DIRSEPARATOR;
   /*double t34;*/      dirc[l1+1] = 0; 
   int i,j,j1, nc, ii, jj;      printf(" DIRC3 = %s \n",dirc);
     }
     for(i=1; i<= nlstate; i++){    ss = strrchr( name, '.' );            /* find last / */
     for(j=1; j<i;j++){    if (ss >0){
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      ss++;
         /*s2 += param[i][j][nc]*cov[nc];*/      strcpy(ext,ss);                     /* save extension */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      l1= strlen( name);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      l2= strlen(ss)+1;
       }      strncpy( finame, name, l1-l2);
       ps[i][j]=s2;      finame[l1-l2]= 0;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    }
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){    return( 0 );                          /* we're done */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  
       }  /******************************************/
       ps[i][j]=s2;  
     }  void replace_back_to_slash(char *s, char*t)
   }  {
     /*ps[3][2]=1;*/    int i;
     int lg=0;
   for(i=1; i<= nlstate; i++){    i=0;
      s1=0;    lg=strlen(t);
     for(j=1; j<i; j++)    for(i=0; i<= lg; i++) {
       s1+=exp(ps[i][j]);      (s[i] = t[i]);
     for(j=i+1; j<=nlstate+ndeath; j++)      if (t[i]== '\\') s[i]='/';
       s1+=exp(ps[i][j]);    }
     ps[i][i]=1./(s1+1.);  }
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  char *trimbb(char *out, char *in)
     for(j=i+1; j<=nlstate+ndeath; j++)  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
       ps[i][j]= exp(ps[i][j])*ps[i][i];    char *s;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    s=out;
   } /* end i */    while (*in != '\0'){
       while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        in++;
     for(jj=1; jj<= nlstate+ndeath; jj++){      }
       ps[ii][jj]=0;      *out++ = *in++;
       ps[ii][ii]=1;    }
     }    *out='\0';
   }    return s;
   }
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  char *cutl(char *blocc, char *alocc, char *in, char occ)
     for(jj=1; jj<= nlstate+ndeath; jj++){  {
      printf("%lf ",ps[ii][jj]);    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
    }       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     printf("\n ");       gives blocc="abcdef2ghi" and alocc="j".
     }       If occ is not found blocc is null and alocc is equal to in. Returns blocc
     printf("\n ");printf("%lf ",cov[2]);*/    */
 /*    char *s, *t, *bl;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    t=in;s=in;
   goto end;*/    while ((*in != occ) && (*in != '\0')){
     return ps;      *alocc++ = *in++;
 }    }
     if( *in == occ){
 /**************** Product of 2 matrices ******************/      *(alocc)='\0';
       s=++in;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    }
 {   
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    if (s == t) {/* occ not found */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      *(alocc-(in-s))='\0';
   /* in, b, out are matrice of pointers which should have been initialized      in=s;
      before: only the contents of out is modified. The function returns    }
      a pointer to pointers identical to out */    while ( *in != '\0'){
   long i, j, k;      *blocc++ = *in++;
   for(i=nrl; i<= nrh; i++)    }
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    *blocc='\0';
         out[i][k] +=in[i][j]*b[j][k];    return t;
   }
   return out;  char *cutv(char *blocc, char *alocc, char *in, char occ)
 }  {
     /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
        and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
 /************* Higher Matrix Product ***************/       gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns alocc
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    */
 {    char *s, *t;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    t=in;s=in;
      duration (i.e. until    while (*in != '\0'){
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      while( *in == occ){
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        *blocc++ = *in++;
      (typically every 2 years instead of every month which is too big).        s=in;
      Model is determined by parameters x and covariates have to be      }
      included manually here.      *blocc++ = *in++;
     }
      */    if (s == t) /* occ not found */
       *(blocc-(in-s))='\0';
   int i, j, d, h, k;    else
   double **out, cov[NCOVMAX];      *(blocc-(in-s)-1)='\0';
   double **newm;    in=s;
     while ( *in != '\0'){
   /* Hstepm could be zero and should return the unit matrix */      *alocc++ = *in++;
   for (i=1;i<=nlstate+ndeath;i++)    }
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);    *alocc='\0';
       po[i][j][0]=(i==j ? 1.0 : 0.0);    return s;
     }  }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){  int nbocc(char *s, char occ)
     for(d=1; d <=hstepm; d++){  {
       newm=savm;    int i,j=0;
       /* Covariates have to be included here again */    int lg=20;
       cov[1]=1.;    i=0;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    lg=strlen(s);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    for(i=0; i<= lg; i++) {
       for (k=1; k<=cptcovage;k++)    if  (s[i] == occ ) j++;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    }
       for (k=1; k<=cptcovprod;k++)    return j;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  }
   
   /* void cutv(char *u,char *v, char*t, char occ) */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  /* { */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  /*      gives u="abcdef2ghi" and v="j" *\/ */
       savm=oldm;  /*   int i,lg,j,p=0; */
       oldm=newm;  /*   i=0; */
     }  /*   lg=strlen(t); */
     for(i=1; i<=nlstate+ndeath; i++)  /*   for(j=0; j<=lg-1; j++) { */
       for(j=1;j<=nlstate+ndeath;j++) {  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
         po[i][j][h]=newm[i][j];  /*   } */
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  /*   for(j=0; j<p; j++) { */
       }  /*     (u[j] = t[j]); */
   } /* end h */  /*   } */
   return po;  /*      u[p]='\0'; */
 }  
   /*    for(j=0; j<= lg; j++) { */
   /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
 /*************** log-likelihood *************/  /*   } */
 double func( double *x)  /* } */
 {  
   int i, ii, j, k, mi, d, kk;  /********************** nrerror ********************/
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;  void nrerror(char error_text[])
   double sw; /* Sum of weights */  {
   double lli; /* Individual log likelihood */    fprintf(stderr,"ERREUR ...\n");
   long ipmx;    fprintf(stderr,"%s\n",error_text);
   /*extern weight */    exit(EXIT_FAILURE);
   /* We are differentiating ll according to initial status */  }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  /*********************** vector *******************/
   /*for(i=1;i<imx;i++)  double *vector(int nl, int nh)
     printf(" %d\n",s[4][i]);  {
   */    double *v;
   cov[1]=1.;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
   for(k=1; k<=nlstate; k++) ll[k]=0.;    return v-nl+NR_END;
   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++){  /************************ free vector ******************/
       for (ii=1;ii<=nlstate+ndeath;ii++)  void free_vector(double*v, int nl, int nh)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  {
       for(d=0; d<dh[mi][i]; d++){    free((FREE_ARG)(v+nl-NR_END));
         newm=savm;  }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {  /************************ivector *******************************/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  int *ivector(long nl,long nh)
         }  {
            int *v;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    if (!v) nrerror("allocation failure in ivector");
         savm=oldm;    return v-nl+NR_END;
         oldm=newm;  }
          
          /******************free ivector **************************/
       } /* end mult */  void free_ivector(int *v, long nl, long nh)
        {
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    free((FREE_ARG)(v+nl-NR_END));
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  }
       ipmx +=1;  
       sw += weight[i];  /************************lvector *******************************/
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  long *lvector(long nl,long nh)
     } /* end of wave */  {
   } /* end of individual */    long *v;
     v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    if (!v) nrerror("allocation failure in ivector");
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    return v-nl+NR_END;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  }
   return -l;  
 }  /******************free lvector **************************/
   void free_lvector(long *v, long nl, long nh)
   {
 /*********** Maximum Likelihood Estimation ***************/    free((FREE_ARG)(v+nl-NR_END));
   }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {  /******************* imatrix *******************************/
   int i,j, iter;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   double **xi,*delti;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   double fret;  { 
   xi=matrix(1,npar,1,npar);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   for (i=1;i<=npar;i++)    int **m; 
     for (j=1;j<=npar;j++)    
       xi[i][j]=(i==j ? 1.0 : 0.0);    /* allocate pointers to rows */ 
   printf("Powell\n");    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   powell(p,xi,npar,ftol,&iter,&fret,func);    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    m -= nrl; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    
     
 }    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 /**** Computes Hessian and covariance matrix ***/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    m[nrl] += NR_END; 
 {    m[nrl] -= ncl; 
   double  **a,**y,*x,pd;    
   double **hess;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   int i, j,jk;    
   int *indx;    /* return pointer to array of pointers to rows */ 
     return m; 
   double hessii(double p[], double delta, int theta, double delti[]);  } 
   double hessij(double p[], double delti[], int i, int j);  
   void lubksb(double **a, int npar, int *indx, double b[]) ;  /****************** free_imatrix *************************/
   void ludcmp(double **a, int npar, int *indx, double *d) ;  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
   hess=matrix(1,npar,1,npar);        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
   printf("\nCalculation of the hessian matrix. Wait...\n");  { 
   for (i=1;i<=npar;i++){    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     printf("%d",i);fflush(stdout);    free((FREE_ARG) (m+nrl-NR_END)); 
     hess[i][i]=hessii(p,ftolhess,i,delti);  } 
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/  /******************* matrix *******************************/
   }  double **matrix(long nrl, long nrh, long ncl, long nch)
    {
   for (i=1;i<=npar;i++) {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     for (j=1;j<=npar;j++)  {    double **m;
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         hess[i][j]=hessij(p,delti,i,j);    if (!m) nrerror("allocation failure 1 in matrix()");
         hess[j][i]=hess[i][j];        m += NR_END;
         /*printf(" %lf ",hess[i][j]);*/    m -= nrl;
       }  
     }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   printf("\n");    m[nrl] += NR_END;
     m[nrl] -= ncl;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  
      for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   a=matrix(1,npar,1,npar);    return m;
   y=matrix(1,npar,1,npar);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   x=vector(1,npar);  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   indx=ivector(1,npar);  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
   for (i=1;i<=npar;i++)     */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  }
   ludcmp(a,npar,indx,&pd);  
   /*************************free matrix ************************/
   for (j=1;j<=npar;j++) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     for (i=1;i<=npar;i++) x[i]=0;  {
     x[j]=1;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     lubksb(a,npar,indx,x);    free((FREE_ARG)(m+nrl-NR_END));
     for (i=1;i<=npar;i++){  }
       matcov[i][j]=x[i];  
     }  /******************* ma3x *******************************/
   }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
   printf("\n#Hessian matrix#\n");    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   for (i=1;i<=npar;i++) {    double ***m;
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
     printf("\n");    m += NR_END;
   }    m -= nrl;
   
   /* Recompute Inverse */    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   for (i=1;i<=npar;i++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    m[nrl] += NR_END;
   ludcmp(a,npar,indx,&pd);    m[nrl] -= ncl;
   
   /*  printf("\n#Hessian matrix recomputed#\n");    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   
   for (j=1;j<=npar;j++) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     for (i=1;i<=npar;i++) x[i]=0;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     x[j]=1;    m[nrl][ncl] += NR_END;
     lubksb(a,npar,indx,x);    m[nrl][ncl] -= nll;
     for (i=1;i<=npar;i++){    for (j=ncl+1; j<=nch; j++) 
       y[i][j]=x[i];      m[nrl][j]=m[nrl][j-1]+nlay;
       printf("%.3e ",y[i][j]);    
     }    for (i=nrl+1; i<=nrh; i++) {
     printf("\n");      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   }      for (j=ncl+1; j<=nch; j++) 
   */        m[i][j]=m[i][j-1]+nlay;
     }
   free_matrix(a,1,npar,1,npar);    return m; 
   free_matrix(y,1,npar,1,npar);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   free_vector(x,1,npar);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   free_ivector(indx,1,npar);    */
   free_matrix(hess,1,npar,1,npar);  }
   
   /*************************free ma3x ************************/
 }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
 /*************** hessian matrix ****************/    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 double hessii( double x[], double delta, int theta, double delti[])    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 {    free((FREE_ARG)(m+nrl-NR_END));
   int i;  }
   int l=1, lmax=20;  
   double k1,k2;  /*************** function subdirf ***********/
   double p2[NPARMAX+1];  char *subdirf(char fileres[])
   double res;  {
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    /* Caution optionfilefiname is hidden */
   double fx;    strcpy(tmpout,optionfilefiname);
   int k=0,kmax=10;    strcat(tmpout,"/"); /* Add to the right */
   double l1;    strcat(tmpout,fileres);
     return tmpout;
   fx=func(x);  }
   for (i=1;i<=npar;i++) p2[i]=x[i];  
   for(l=0 ; l <=lmax; l++){  /*************** function subdirf2 ***********/
     l1=pow(10,l);  char *subdirf2(char fileres[], char *preop)
     delts=delt;  {
     for(k=1 ; k <kmax; k=k+1){    
       delt = delta*(l1*k);    /* Caution optionfilefiname is hidden */
       p2[theta]=x[theta] +delt;    strcpy(tmpout,optionfilefiname);
       k1=func(p2)-fx;    strcat(tmpout,"/");
       p2[theta]=x[theta]-delt;    strcat(tmpout,preop);
       k2=func(p2)-fx;    strcat(tmpout,fileres);
       /*res= (k1-2.0*fx+k2)/delt/delt; */    return tmpout;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  }
        
 #ifdef DEBUG  /*************** function subdirf3 ***********/
       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);  char *subdirf3(char fileres[], char *preop, char *preop2)
 #endif  {
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    /* Caution optionfilefiname is hidden */
         k=kmax;    strcpy(tmpout,optionfilefiname);
       }    strcat(tmpout,"/");
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    strcat(tmpout,preop);
         k=kmax; l=lmax*10.;    strcat(tmpout,preop2);
       }    strcat(tmpout,fileres);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    return tmpout;
         delts=delt;  }
       }  
     }  /***************** f1dim *************************/
   }  extern int ncom; 
   delti[theta]=delts;  extern double *pcom,*xicom;
   return res;  extern double (*nrfunc)(double []); 
     
 }  double f1dim(double x) 
   { 
 double hessij( double x[], double delti[], int thetai,int thetaj)    int j; 
 {    double f;
   int i;    double *xt; 
   int l=1, l1, lmax=20;   
   double k1,k2,k3,k4,res,fx;    xt=vector(1,ncom); 
   double p2[NPARMAX+1];    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   int k;    f=(*nrfunc)(xt); 
     free_vector(xt,1,ncom); 
   fx=func(x);    return f; 
   for (k=1; k<=2; k++) {  } 
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;  /*****************brent *************************/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     k1=func(p2)-fx;  { 
      int iter; 
     p2[thetai]=x[thetai]+delti[thetai]/k;    double a,b,d,etemp;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    double fu,fv,fw,fx;
     k2=func(p2)-fx;    double ftemp;
      double p,q,r,tol1,tol2,u,v,w,x,xm; 
     p2[thetai]=x[thetai]-delti[thetai]/k;    double e=0.0; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;   
     k3=func(p2)-fx;    a=(ax < cx ? ax : cx); 
      b=(ax > cx ? ax : cx); 
     p2[thetai]=x[thetai]-delti[thetai]/k;    x=w=v=bx; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    fw=fv=fx=(*f)(x); 
     k4=func(p2)-fx;    for (iter=1;iter<=ITMAX;iter++) { 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      xm=0.5*(a+b); 
 #ifdef DEBUG      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     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);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 #endif      printf(".");fflush(stdout);
   }      fprintf(ficlog,".");fflush(ficlog);
   return res;  #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);
       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);
 /************** Inverse of matrix **************/      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 void ludcmp(double **a, int n, int *indx, double *d)  #endif
 {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   int i,imax,j,k;        *xmin=x; 
   double big,dum,sum,temp;        return fx; 
   double *vv;      } 
        ftemp=fu;
   vv=vector(1,n);      if (fabs(e) > tol1) { 
   *d=1.0;        r=(x-w)*(fx-fv); 
   for (i=1;i<=n;i++) {        q=(x-v)*(fx-fw); 
     big=0.0;        p=(x-v)*q-(x-w)*r; 
     for (j=1;j<=n;j++)        q=2.0*(q-r); 
       if ((temp=fabs(a[i][j])) > big) big=temp;        if (q > 0.0) p = -p; 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        q=fabs(q); 
     vv[i]=1.0/big;        etemp=e; 
   }        e=d; 
   for (j=1;j<=n;j++) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     for (i=1;i<j;i++) {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       sum=a[i][j];        else { 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          d=p/q; 
       a[i][j]=sum;          u=x+d; 
     }          if (u-a < tol2 || b-u < tol2) 
     big=0.0;            d=SIGN(tol1,xm-x); 
     for (i=j;i<=n;i++) {        } 
       sum=a[i][j];      } else { 
       for (k=1;k<j;k++)        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         sum -= a[i][k]*a[k][j];      } 
       a[i][j]=sum;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       if ( (dum=vv[i]*fabs(sum)) >= big) {      fu=(*f)(u); 
         big=dum;      if (fu <= fx) { 
         imax=i;        if (u >= x) a=x; else b=x; 
       }        SHFT(v,w,x,u) 
     }          SHFT(fv,fw,fx,fu) 
     if (j != imax) {          } else { 
       for (k=1;k<=n;k++) {            if (u < x) a=u; else b=u; 
         dum=a[imax][k];            if (fu <= fw || w == x) { 
         a[imax][k]=a[j][k];              v=w; 
         a[j][k]=dum;              w=u; 
       }              fv=fw; 
       *d = -(*d);              fw=fu; 
       vv[imax]=vv[j];            } else if (fu <= fv || v == x || v == w) { 
     }              v=u; 
     indx[j]=imax;              fv=fu; 
     if (a[j][j] == 0.0) a[j][j]=TINY;            } 
     if (j != n) {          } 
       dum=1.0/(a[j][j]);    } 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    nrerror("Too many iterations in brent"); 
     }    *xmin=x; 
   }    return fx; 
   free_vector(vv,1,n);  /* Doesn't work */  } 
 ;  
 }  /****************** mnbrak ***********************/
   
 void lubksb(double **a, int n, int *indx, double b[])  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 {              double (*func)(double)) 
   int i,ii=0,ip,j;  { 
   double sum;    double ulim,u,r,q, dum;
      double fu; 
   for (i=1;i<=n;i++) {   
     ip=indx[i];    *fa=(*func)(*ax); 
     sum=b[ip];    *fb=(*func)(*bx); 
     b[ip]=b[i];    if (*fb > *fa) { 
     if (ii)      SHFT(dum,*ax,*bx,dum) 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        SHFT(dum,*fb,*fa,dum) 
     else if (sum) ii=i;        } 
     b[i]=sum;    *cx=(*bx)+GOLD*(*bx-*ax); 
   }    *fc=(*func)(*cx); 
   for (i=n;i>=1;i--) {    while (*fb > *fc) { 
     sum=b[i];      r=(*bx-*ax)*(*fb-*fc); 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      q=(*bx-*cx)*(*fb-*fa); 
     b[i]=sum/a[i][i];      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
 /************ Frequencies ********************/        fu=(*func)(u); 
 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)      } else if ((*cx-u)*(u-ulim) > 0.0) { 
 {  /* Some frequencies */        fu=(*func)(u); 
          if (fu < *fc) { 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double ***freq; /* Frequencies */            SHFT(*fb,*fc,fu,(*func)(u)) 
   double *pp;            } 
   double pos, k2, dateintsum=0,k2cpt=0;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   FILE *ficresp;        u=ulim; 
   char fileresp[FILENAMELENGTH];        fu=(*func)(u); 
        } else { 
   pp=vector(1,nlstate);        u=(*cx)+GOLD*(*cx-*bx); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        fu=(*func)(u); 
   strcpy(fileresp,"p");      } 
   strcat(fileresp,fileres);      SHFT(*ax,*bx,*cx,u) 
   if((ficresp=fopen(fileresp,"w"))==NULL) {        SHFT(*fa,*fb,*fc,fu) 
     printf("Problem with prevalence resultfile: %s\n", fileresp);        } 
     exit(0);  } 
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  /*************** linmin ************************/
   j1=0;  
    int ncom; 
   j=cptcoveff;  double *pcom,*xicom;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  double (*nrfunc)(double []); 
     
   for(k1=1; k1<=j;k1++){  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     for(i1=1; i1<=ncodemax[k1];i1++){  { 
       j1++;    double brent(double ax, double bx, double cx, 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);                 double (*f)(double), double tol, double *xmin); 
         scanf("%d", i);*/    double f1dim(double x); 
       for (i=-1; i<=nlstate+ndeath; i++)      void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         for (jk=-1; jk<=nlstate+ndeath; jk++)                  double *fc, double (*func)(double)); 
           for(m=agemin; m <= agemax+3; m++)    int j; 
             freq[i][jk][m]=0;    double xx,xmin,bx,ax; 
          double fx,fb,fa;
       dateintsum=0;   
       k2cpt=0;    ncom=n; 
       for (i=1; i<=imx; i++) {    pcom=vector(1,n); 
         bool=1;    xicom=vector(1,n); 
         if  (cptcovn>0) {    nrfunc=func; 
           for (z1=1; z1<=cptcoveff; z1++)    for (j=1;j<=n;j++) { 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      pcom[j]=p[j]; 
               bool=0;      xicom[j]=xi[j]; 
         }    } 
         if (bool==1) {    ax=0.0; 
           for(m=firstpass; m<=lastpass; m++){    xx=1.0; 
             k2=anint[m][i]+(mint[m][i]/12.);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
               if(agev[m][i]==0) agev[m][i]=agemax+1;  #ifdef DEBUG
               if(agev[m][i]==1) agev[m][i]=agemax+2;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
               if (m<lastpass) {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  #endif
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    for (j=1;j<=n;j++) { 
               }      xi[j] *= xmin; 
                    p[j] += xi[j]; 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    } 
                 dateintsum=dateintsum+k2;    free_vector(xicom,1,n); 
                 k2cpt++;    free_vector(pcom,1,n); 
               }  } 
             }  
           }  char *asc_diff_time(long time_sec, char ascdiff[])
         }  {
       }    long sec_left, days, hours, minutes;
            days = (time_sec) / (60*60*24);
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
       if  (cptcovn>0) {    sec_left = (sec_left) %(60*60);
         fprintf(ficresp, "\n#********** Variable ");    minutes = (sec_left) /60;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    sec_left = (sec_left) % (60);
         fprintf(ficresp, "**********\n#");    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
       }    return ascdiff;
       for(i=1; i<=nlstate;i++)  }
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
       fprintf(ficresp, "\n");  /*************** powell ************************/
        void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       for(i=(int)agemin; i <= (int)agemax+3; i++){              double (*func)(double [])) 
         if(i==(int)agemax+3)  { 
           printf("Total");    void linmin(double p[], double xi[], int n, double *fret, 
         else                double (*func)(double [])); 
           printf("Age %d", i);    int i,ibig,j; 
         for(jk=1; jk <=nlstate ; jk++){    double del,t,*pt,*ptt,*xit;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double fp,fptt;
             pp[jk] += freq[jk][m][i];    double *xits;
         }    int niterf, itmp;
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)    pt=vector(1,n); 
             pos += freq[jk][m][i];    ptt=vector(1,n); 
           if(pp[jk]>=1.e-10)    xit=vector(1,n); 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    xits=vector(1,n); 
           else    *fret=(*func)(p); 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    for (j=1;j<=n;j++) pt[j]=p[j]; 
         }      rcurr_time = time(NULL);  
     for (*iter=1;;++(*iter)) { 
         for(jk=1; jk <=nlstate ; jk++){      fp=(*fret); 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      ibig=0; 
             pp[jk] += freq[jk][m][i];      del=0.0; 
         }      rlast_time=rcurr_time;
       /* (void) gettimeofday(&curr_time,&tzp); */
         for(jk=1,pos=0; jk <=nlstate ; jk++)      rcurr_time = time(NULL);  
           pos += pp[jk];      curr_time = *localtime(&rcurr_time);
         for(jk=1; jk <=nlstate ; jk++){      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
           if(pos>=1.e-5)      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
           else     for (i=1;i<=n;i++) {
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        printf(" %d %.12f",i, p[i]);
           if( i <= (int) agemax){        fprintf(ficlog," %d %.12lf",i, p[i]);
             if(pos>=1.e-5){        fprintf(ficrespow," %.12lf", p[i]);
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      }
               probs[i][jk][j1]= pp[jk]/pos;      printf("\n");
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      fprintf(ficlog,"\n");
             }      fprintf(ficrespow,"\n");fflush(ficrespow);
             else      if(*iter <=3){
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        tml = *localtime(&rcurr_time);
           }        strcpy(strcurr,asctime(&tml));
         }  /*       asctime_r(&tm,strcurr); */
                rforecast_time=rcurr_time; 
         for(jk=-1; jk <=nlstate+ndeath; jk++)        itmp = strlen(strcurr);
           for(m=-1; m <=nlstate+ndeath; m++)        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          strcurr[itmp-1]='\0';
         if(i <= (int) agemax)        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
           fprintf(ficresp,"\n");        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
         printf("\n");        for(niterf=10;niterf<=30;niterf+=10){
       }          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
     }          forecast_time = *localtime(&rforecast_time);
   }  /*      asctime_r(&tmf,strfor); */
   dateintmean=dateintsum/k2cpt;          strcpy(strfor,asctime(&forecast_time));
            itmp = strlen(strfor);
   fclose(ficresp);          if(strfor[itmp-1]=='\n')
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          strfor[itmp-1]='\0';
   free_vector(pp,1,nlstate);          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);
   /* End of Freq */        }
 }      }
       for (i=1;i<=n;i++) { 
 /************ Prevalence ********************/        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 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)        fptt=(*fret); 
 {  /* Some frequencies */  #ifdef DEBUG
          printf("fret=%lf \n",*fret);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        fprintf(ficlog,"fret=%lf \n",*fret);
   double ***freq; /* Frequencies */  #endif
   double *pp;        printf("%d",i);fflush(stdout);
   double pos, k2;        fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
   pp=vector(1,nlstate);        if (fabs(fptt-(*fret)) > del) { 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          del=fabs(fptt-(*fret)); 
            ibig=i; 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        } 
   j1=0;  #ifdef DEBUG
          printf("%d %.12e",i,(*fret));
   j=cptcoveff;        fprintf(ficlog,"%d %.12e",i,(*fret));
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        for (j=1;j<=n;j++) {
            xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
  for(k1=1; k1<=j;k1++){          printf(" x(%d)=%.12e",j,xit[j]);
     for(i1=1; i1<=ncodemax[k1];i1++){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       j1++;        }
          for(j=1;j<=n;j++) {
       for (i=-1; i<=nlstate+ndeath; i++)            printf(" p=%.12e",p[j]);
         for (jk=-1; jk<=nlstate+ndeath; jk++)            fprintf(ficlog," p=%.12e",p[j]);
           for(m=agemin; m <= agemax+3; m++)        }
             freq[i][jk][m]=0;        printf("\n");
              fprintf(ficlog,"\n");
       for (i=1; i<=imx; i++) {  #endif
         bool=1;      } 
         if  (cptcovn>0) {      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
           for (z1=1; z1<=cptcoveff; z1++)  #ifdef DEBUG
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        int k[2],l;
               bool=0;        k[0]=1;
         }        k[1]=-1;
         if (bool==1) {        printf("Max: %.12e",(*func)(p));
           for(m=firstpass; m<=lastpass; m++){        fprintf(ficlog,"Max: %.12e",(*func)(p));
             k2=anint[m][i]+(mint[m][i]/12.);        for (j=1;j<=n;j++) {
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          printf(" %.12e",p[j]);
               if(agev[m][i]==0) agev[m][i]=agemax+1;          fprintf(ficlog," %.12e",p[j]);
               if(agev[m][i]==1) agev[m][i]=agemax+2;        }
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        printf("\n");
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */        fprintf(ficlog,"\n");
             }        for(l=0;l<=1;l++) {
           }          for (j=1;j<=n;j++) {
         }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         for(i=(int)agemin; i <= (int)agemax+3; i++){            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           for(jk=1; jk <=nlstate ; jk++){          }
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
               pp[jk] += freq[jk][m][i];          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           }        }
           for(jk=1; jk <=nlstate ; jk++){  #endif
             for(m=-1, pos=0; m <=0 ; m++)  
             pos += freq[jk][m][i];  
         }        free_vector(xit,1,n); 
                free_vector(xits,1,n); 
          for(jk=1; jk <=nlstate ; jk++){        free_vector(ptt,1,n); 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        free_vector(pt,1,n); 
              pp[jk] += freq[jk][m][i];        return; 
          }      } 
                if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
          for(jk=1; jk <=nlstate ; jk++){                  xit[j]=p[j]-pt[j]; 
            if( i <= (int) agemax){        pt[j]=p[j]; 
              if(pos>=1.e-5){      } 
                probs[i][jk][j1]= pp[jk]/pos;      fptt=(*func)(ptt); 
              }      if (fptt < fp) { 
            }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
          }        if (t < 0.0) { 
                    linmin(p,xit,n,fret,func); 
         }          for (j=1;j<=n;j++) { 
     }            xi[j][ibig]=xi[j][n]; 
   }            xi[j][n]=xit[j]; 
            }
    #ifdef DEBUG
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   free_vector(pp,1,nlstate);          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++){
 }  /* End of Freq */            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
 /************* Waves Concatenation ***************/          }
           printf("\n");
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          fprintf(ficlog,"\n");
 {  #endif
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        }
      Death is a valid wave (if date is known).      } 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    } 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  } 
      and mw[mi+1][i]. dh depends on stepm.  
      */  /**** Prevalence limit (stable or period prevalence)  ****************/
   
   int i, mi, m;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  {
      double sum=0., jmean=0.;*/    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
   int j, k=0,jk, ju, jl;  
   double sum=0.;    int i, ii,j,k;
   jmin=1e+5;    double min, max, maxmin, maxmax,sumnew=0.;
   jmax=-1;    /* double **matprod2(); */ /* test */
   jmean=0.;    double **out, cov[NCOVMAX+1], **pmij();
   for(i=1; i<=imx; i++){    double **newm;
     mi=0;    double agefin, delaymax=50 ; /* Max number of years to converge */
     m=firstpass;  
     while(s[m][i] <= nlstate){    for (ii=1;ii<=nlstate+ndeath;ii++)
       if(s[m][i]>=1)      for (j=1;j<=nlstate+ndeath;j++){
         mw[++mi][i]=m;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if(m >=lastpass)      }
         break;  
       else     cov[1]=1.;
         m++;   
     }/* end while */   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     if (s[m][i] > nlstate){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       mi++;     /* Death is another wave */      newm=savm;
       /* if(mi==0)  never been interviewed correctly before death */      /* Covariates have to be included here again */
          /* Only death is a correct wave */      cov[2]=agefin;
       mw[mi][i]=m;      
     }      for (k=1; k<=cptcovn;k++) {
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     wav[i]=mi;        /*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(mi==0)      }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   }      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
       /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
   for(i=1; i<=imx; i++){      
     for(mi=1; mi<wav[i];mi++){      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       if (stepm <=0)      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         dh[mi][i]=1;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       else{      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         if (s[mw[mi+1][i]][i] > nlstate) {      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
           if (agedc[i] < 2*AGESUP) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      
           if(j==0) j=1;  /* Survives at least one month after exam */      savm=oldm;
           k=k+1;      oldm=newm;
           if (j >= jmax) jmax=j;      maxmax=0.;
           if (j <= jmin) jmin=j;      for(j=1;j<=nlstate;j++){
           sum=sum+j;        min=1.;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        max=0.;
           }        for(i=1; i<=nlstate; i++) {
         }          sumnew=0;
         else{          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          prlim[i][j]= newm[i][j]/(1-sumnew);
           k=k+1;          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
           if (j >= jmax) jmax=j;          max=FMAX(max,prlim[i][j]);
           else if (j <= jmin)jmin=j;          min=FMIN(min,prlim[i][j]);
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        }
           sum=sum+j;        maxmin=max-min;
         }        maxmax=FMAX(maxmax,maxmin);
         jk= j/stepm;      }
         jl= j -jk*stepm;      if(maxmax < ftolpl){
         ju= j -(jk+1)*stepm;        return prlim;
         if(jl <= -ju)      }
           dh[mi][i]=jk;    }
         else  }
           dh[mi][i]=jk+1;  
         if(dh[mi][i]==0)  /*************** transition probabilities ***************/ 
           dh[mi][i]=1; /* At least one step */  
       }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     }  {
   }    /* According to parameters values stored in x and the covariate's values stored in cov,
   jmean=sum/k;       computes the probability to be observed in state j being in state i by appying the
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);       model to the ncovmodel covariates (including constant and age).
  }       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
 /*********** Tricode ****************************/       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
 void tricode(int *Tvar, int **nbcode, int imx)       ncth covariate in the global vector x is given by the formula:
 {       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
   int Ndum[20],ij=1, k, j, i;       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
   int cptcode=0;       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
   cptcoveff=0;       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
         Outputs ps[i][j] the probability to be observed in j being in j according to
   for (k=0; k<19; k++) Ndum[k]=0;       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   for (k=1; k<=7; k++) ncodemax[k]=0;    */
     double s1, lnpijopii;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    /*double t34;*/
     for (i=1; i<=imx; i++) {    int i,j,j1, nc, ii, jj;
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;      for(i=1; i<= nlstate; i++){
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        for(j=1; j<i;j++){
       if (ij > cptcode) cptcode=ij;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     }            /*lnpijopii += param[i][j][nc]*cov[nc];*/
             lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
     for (i=0; i<=cptcode; i++) {  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       if(Ndum[i]!=0) ncodemax[j]++;          }
     }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     ij=1;  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         }
         for(j=i+1; j<=nlstate+ndeath;j++){
     for (i=1; i<=ncodemax[j]; i++) {          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       for (k=0; k<=19; k++) {            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
         if (Ndum[k] != 0) {            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
           nbcode[Tvar[j]][ij]=k;  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/          }
           ij++;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         }        }
         if (ij > ncodemax[j]) break;      }
       }        
     }      for(i=1; i<= nlstate; i++){
   }          s1=0;
         for(j=1; j<i; j++){
  for (k=0; k<19; k++) Ndum[k]=0;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
  for (i=1; i<=ncovmodel-2; i++) {        }
       ij=Tvar[i];        for(j=i+1; j<=nlstate+ndeath; j++){
       Ndum[ij]++;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     }          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }
  ij=1;        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
  for (i=1; i<=10; i++) {        ps[i][i]=1./(s1+1.);
    if((Ndum[i]!=0) && (i<=ncovcol)){        /* Computing other pijs */
      Tvaraff[ij]=i;        for(j=1; j<i; j++)
      ij++;          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 */
     cptcoveff=ij-1;      } /* end i */
 }      
       for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
 /*********** Health Expectancies ****************/        for(jj=1; jj<= nlstate+ndeath; jj++){
           ps[ii][jj]=0;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          ps[ii][ii]=1;
 {        }
   /* Health expectancies */      }
   int i, j, nhstepm, hstepm, h, nstepm, k;      
   double age, agelim, hf;      
   double ***p3mat;      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
        /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   fprintf(ficreseij,"# Health expectancies\n");      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
   fprintf(ficreseij,"# Age");      /*   } */
   for(i=1; i<=nlstate;i++)      /*   printf("\n "); */
     for(j=1; j<=nlstate;j++)      /* } */
       fprintf(ficreseij," %1d-%1d",i,j);      /* printf("\n ");printf("%lf ",cov[2]);*/
   fprintf(ficreseij,"\n");      /*
         for(i=1; i<= npar; i++) printf("%f ",x[i]);
   k=1;             /* For example stepm=6 months */        goto end;*/
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */      return ps;
   hstepm=stepm;   /* or (b) 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  /**************** Product of 2 matrices ******************/
      nstepm is the number of stepm from age to agelin.  
      Look at hpijx to understand the reason of that which relies in memory size  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
      and note for a fixed period like k years */  {
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
      survival function given by stepm (the optimization length). Unfortunately it       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
      means that if the survival funtion is printed only each two years of age and if    /* in, b, out are matrice of pointers which should have been initialized 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same       before: only the contents of out is modified. The function returns
      results. So we changed our mind and took the option of the best precision.       a pointer to pointers identical to out */
   */    int i, j, k;
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */    for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++){
   agelim=AGESUP;        out[i][k]=0.;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        for(j=ncl; j<=nch; j++)
     /* nhstepm age range expressed in number of stepm */          out[i][k] +=in[i][j]*b[j][k];
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      }
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    return out;
     /* if (stepm >= YEARM) hstepm=1;*/  }
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  /************* Higher Matrix Product ***************/
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  {
     for(i=1; i<=nlstate;i++)    /* Computes the transition matrix starting at age 'age' over 
       for(j=1; j<=nlstate;j++)       'nhstepm*hstepm*stepm' months (i.e. until
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;       nhstepm*hstepm matrices. 
           /* 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]);*/       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         }       (typically every 2 years instead of every month which is too big 
     fprintf(ficreseij,"%3.0f",age );       for the memory).
     for(i=1; i<=nlstate;i++)       Model is determined by parameters x and covariates have to be 
       for(j=1; j<=nlstate;j++){       included manually here. 
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);  
       }       */
     fprintf(ficreseij,"\n");  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i, j, d, h, k;
   }    double **out, cov[NCOVMAX+1];
 }    double **newm;
   
 /************ Variance ******************/    /* Hstepm could be zero and should return the unit matrix */
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    for (i=1;i<=nlstate+ndeath;i++)
 {      for (j=1;j<=nlstate+ndeath;j++){
   /* Variance of health expectancies */        oldm[i][j]=(i==j ? 1.0 : 0.0);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        po[i][j][0]=(i==j ? 1.0 : 0.0);
   double **newm;      }
   double **dnewm,**doldm;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   int i, j, nhstepm, hstepm, h, nstepm, kk;    for(h=1; h <=nhstepm; h++){
   int k, cptcode;      for(d=1; d <=hstepm; d++){
   double *xp;        newm=savm;
   double **gp, **gm;        /* Covariates have to be included here again */
   double ***gradg, ***trgradg;        cov[1]=1.;
   double ***p3mat;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double age,agelim, hf;        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(ficresvij,"# Covariances of life expectancies\n");          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   fprintf(ficresvij,"# 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]]];
     for(j=1; j<=nlstate;j++)  
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  
   fprintf(ficresvij,"\n");        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   xp=vector(1,npar);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   dnewm=matrix(1,nlstate,1,npar);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   doldm=matrix(1,nlstate,1,nlstate);        savm=oldm;
          oldm=newm;
   kk=1;             /* For example stepm=6 months */      }
   hstepm=kk*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */      for(i=1; i<=nlstate+ndeath; i++)
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */        for(j=1;j<=nlstate+ndeath;j++) {
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          po[i][j][h]=newm[i][j];
      nhstepm is the number of hstepm from age to agelim          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
      nstepm is the number of stepm from age to agelin.        }
      Look at hpijx to understand the reason of that which relies in memory size      /*printf("h=%d ",h);*/
      and note for a fixed period like k years */    } /* end h */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  /*     printf("\n H=%d \n",h); */
      survival function given by stepm (the optimization length). Unfortunately it    return po;
      means that if the survival funtion is printed only each two years of age and if  }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  
      results. So we changed our mind and took the option of the best precision.  
   */  /*************** log-likelihood *************/
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */  double func( double *x)
   agelim = AGESUP;  {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int i, ii, j, k, mi, d, kk;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    double **out;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double sw; /* Sum of weights */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    double lli; /* Individual log likelihood */
     gp=matrix(0,nhstepm,1,nlstate);    int s1, s2;
     gm=matrix(0,nhstepm,1,nlstate);    double bbh, survp;
     long ipmx;
     for(theta=1; theta <=npar; theta++){    /*extern weight */
       for(i=1; i<=npar; i++){ /* Computes gradient */    /* We are differentiating ll according to initial status */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       }    /*for(i=1;i<imx;i++) 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        printf(" %d\n",s[4][i]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    */
     cov[1]=1.;
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
           prlim[i][i]=probs[(int)age][i][ij];  
       }    if(mle==1){
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(j=1; j<= nlstate; j++){        /* Computes the values of the ncovmodel covariates of the model
         for(h=0; h<=nhstepm; h++){           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];           to be observed in j being in i according to the model.
         }         */
       }        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
              cov[2+k]=covar[Tvar[k]][i];
       for(i=1; i<=npar; i++) /* Computes gradient */        }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);             is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);           has been calculated etc */
          for(mi=1; mi<= wav[i]-1; mi++){
       if (popbased==1) {          for (ii=1;ii<=nlstate+ndeath;ii++)
         for(i=1; i<=nlstate;i++)            for (j=1;j<=nlstate+ndeath;j++){
           prlim[i][i]=probs[(int)age][i][ij];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
       for(j=1; j<= nlstate; j++){          for(d=0; d<dh[mi][i]; d++){
         for(h=0; h<=nhstepm; h++){            newm=savm;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
       }            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(j=1; j<= nlstate; j++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(h=0; h<=nhstepm; h++){            savm=oldm;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            oldm=newm;
         }          } /* end mult */
     } /* End theta */        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          /* 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(h=0; h<=nhstepm; h++)           * (in months) between two waves is not a multiple of stepm, we rounded to 
       for(j=1; j<=nlstate;j++)           * the nearest (and in case of equal distance, to the lowest) interval but now
         for(theta=1; theta <=npar; theta++)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           trgradg[h][j][theta]=gradg[h][theta][j];           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     for(i=1;i<=nlstate;i++)           * -stepm/2 to stepm/2 .
       for(j=1;j<=nlstate;j++)           * For stepm=1 the results are the same as for previous versions of Imach.
         vareij[i][j][(int)age] =0.;           * For stepm > 1 the results are less biased than in previous versions. 
            */
     for(h=0;h<=nhstepm;h++){          s1=s[mw[mi][i]][i];
       for(k=0;k<=nhstepm;k++){          s2=s[mw[mi+1][i]][i];
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          bbh=(double)bh[mi][i]/(double)stepm; 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          /* bias bh is positive if real duration
         for(i=1;i<=nlstate;i++)           * is higher than the multiple of stepm and negative otherwise.
           for(j=1;j<=nlstate;j++)           */
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          /* 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){ 
     }            /* i.e. if s2 is a death state and if the date of death is known 
                then the contribution to the likelihood is the probability to 
     fprintf(ficresvij,"%.0f ",age );               die between last step unit time and current  step unit time, 
     for(i=1; i<=nlstate;i++)               which is also equal to probability to die before dh 
       for(j=1; j<=nlstate;j++){               minus probability to die before dh-stepm . 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);               In version up to 0.92 likelihood was computed
       }          as if date of death was unknown. Death was treated as any other
     fprintf(ficresvij,"\n");          health state: the date of the interview describes the actual state
     free_matrix(gp,0,nhstepm,1,nlstate);          and not the date of a change in health state. The former idea was
     free_matrix(gm,0,nhstepm,1,nlstate);          to consider that at each interview the state was recorded
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          (healthy, disable or death) and IMaCh was corrected; but when we
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          introduced the exact date of death then we should have modified
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          the contribution of an exact death to the likelihood. This new
   } /* End age */          contribution is smaller and very dependent of the step unit
            stepm. It is no more the probability to die between last interview
   free_vector(xp,1,npar);          and month of death but the probability to survive from last
   free_matrix(doldm,1,nlstate,1,npar);          interview up to one month before death multiplied by the
   free_matrix(dnewm,1,nlstate,1,nlstate);          probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
 }          mortality artificially. The bad side is that we add another loop
           which slows down the processing. The difference can be up to 10%
 /************ Variance of prevlim ******************/          lower mortality.
 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)            */
 {            lli=log(out[s1][s2] - savm[s1][s2]);
   /* Variance of prevalence limit */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;          } else if  (s2==-2) {
   double **dnewm,**doldm;            for (j=1,survp=0. ; j<=nlstate; j++) 
   int i, j, nhstepm, hstepm;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   int k, cptcode;            /*survp += out[s1][j]; */
   double *xp;            lli= log(survp);
   double *gp, *gm;          }
   double **gradg, **trgradg;          
   double age,agelim;          else if  (s2==-4) { 
   int theta;            for (j=3,survp=0. ; j<=nlstate; j++)  
                  survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");            lli= log(survp); 
   fprintf(ficresvpl,"# Age");          } 
   for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %1d-%1d",i,i);          else if  (s2==-5) { 
   fprintf(ficresvpl,"\n");            for (j=1,survp=0. ; j<=2; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   xp=vector(1,npar);            lli= log(survp); 
   dnewm=matrix(1,nlstate,1,npar);          } 
   doldm=matrix(1,nlstate,1,nlstate);          
            else{
   hstepm=1*YEARM; /* Every year of age */            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            /*  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 */
   agelim = AGESUP;          } 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          /*if(lli ==000.0)*/
     if (stepm >= YEARM) hstepm=1;          /*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); */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          ipmx +=1;
     gradg=matrix(1,npar,1,nlstate);          sw += weight[i];
     gp=vector(1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     gm=vector(1,nlstate);        } /* end of wave */
       } /* end of individual */
     for(theta=1; theta <=npar; theta++){    }  else if(mle==2){
       for(i=1; i<=npar; i++){ /* Computes gradient */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }        for(mi=1; mi<= wav[i]-1; mi++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(i=1;i<=nlstate;i++)            for (j=1;j<=nlstate+ndeath;j++){
         gp[i] = prlim[i][i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                  savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1; i<=npar; i++) /* Computes gradient */            }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          for(d=0; d<=dh[mi][i]; d++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            newm=savm;
       for(i=1;i<=nlstate;i++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         gm[i] = prlim[i][i];            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(i=1;i<=nlstate;i++)            }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     } /* End theta */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     trgradg =matrix(1,nlstate,1,npar);            oldm=newm;
           } /* end mult */
     for(j=1; j<=nlstate;j++)        
       for(theta=1; theta <=npar; theta++)          s1=s[mw[mi][i]][i];
         trgradg[j][theta]=gradg[theta][j];          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
     for(i=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 */
       varpl[i][(int)age] =0.;          ipmx +=1;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          sw += weight[i];
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(i=1;i<=nlstate;i++)        } /* end of wave */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      } /* end of individual */
     }  else if(mle==3){  /* exponential inter-extrapolation */
     fprintf(ficresvpl,"%.0f ",age );      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(i=1; i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        for(mi=1; mi<= wav[i]-1; mi++){
     fprintf(ficresvpl,"\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
     free_vector(gp,1,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
     free_vector(gm,1,nlstate);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_matrix(gradg,1,npar,1,nlstate);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_matrix(trgradg,1,nlstate,1,npar);            }
   } /* End age */          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   free_vector(xp,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_matrix(doldm,1,nlstate,1,npar);            for (kk=1; kk<=cptcovage;kk++) {
   free_matrix(dnewm,1,nlstate,1,nlstate);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
 }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /************ Variance of one-step probabilities  ******************/            savm=oldm;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)            oldm=newm;
 {          } /* end mult */
   int i, j;        
   int k=0, cptcode;          s1=s[mw[mi][i]][i];
   double **dnewm,**doldm;          s2=s[mw[mi+1][i]][i];
   double *xp;          bbh=(double)bh[mi][i]/(double)stepm; 
   double *gp, *gm;          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 */
   double **gradg, **trgradg;          ipmx +=1;
   double age,agelim, cov[NCOVMAX];          sw += weight[i];
   int theta;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char fileresprob[FILENAMELENGTH];        } /* end of wave */
       } /* end of individual */
   strcpy(fileresprob,"prob");    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   strcat(fileresprob,fileres);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     printf("Problem with resultfile: %s\n", fileresprob);        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   xp=vector(1,npar);            }
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          for(d=0; d<dh[mi][i]; d++){
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   cov[1]=1;            for (kk=1; kk<=cptcovage;kk++) {
   for (age=bage; age<=fage; age ++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     cov[2]=age;            }
     gradg=matrix(1,npar,1,9);          
     trgradg=matrix(1,9,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            savm=oldm;
                oldm=newm;
     for(theta=1; theta <=npar; theta++){          } /* end mult */
       for(i=1; i<=npar; i++)        
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          s1=s[mw[mi][i]][i];
                s2=s[mw[mi+1][i]][i];
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          if( s2 > nlstate){ 
                lli=log(out[s1][s2] - savm[s1][s2]);
       k=0;          }else{
       for(i=1; i<= (nlstate+ndeath); i++){            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         for(j=1; j<=(nlstate+ndeath);j++){          }
            k=k+1;          ipmx +=1;
           gp[k]=pmmij[i][j];          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]); */
         } /* end of wave */
       for(i=1; i<=npar; i++)      } /* end of individual */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
          for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
       k=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(i=1; i<=(nlstate+ndeath); i++){            for (j=1;j<=nlstate+ndeath;j++){
         for(j=1; j<=(nlstate+ndeath);j++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           k=k+1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           gm[k]=pmmij[i][j];            }
         }          for(d=0; d<dh[mi][i]; d++){
       }            newm=savm;
                  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)            for (kk=1; kk<=cptcovage;kk++) {
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }            }
           
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(theta=1; theta <=npar; theta++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       trgradg[j][theta]=gradg[theta][j];            savm=oldm;
              oldm=newm;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          } /* end mult */
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        
           s1=s[mw[mi][i]][i];
      pmij(pmmij,cov,ncovmodel,x,nlstate);          s2=s[mw[mi+1][i]][i];
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
      k=0;          ipmx +=1;
      for(i=1; i<=(nlstate+ndeath); i++){          sw += weight[i];
        for(j=1; j<=(nlstate+ndeath);j++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          k=k+1;          /*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]);*/
          gm[k]=pmmij[i][j];        } /* end of wave */
         }      } /* end of individual */
      }    } /* End of if */
          for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      /*printf("\n%d ",(int)age);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
            return -l;
   }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  
      }*/  /*************** log-likelihood *************/
   double funcone( double *x)
   fprintf(ficresprob,"\n%d ",(int)age);  {
     /* Same as likeli but slower because of a lot of printf and if */
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    int i, ii, j, k, mi, d, kk;
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    double **out;
   }    double lli; /* Individual log likelihood */
     double llt;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    int s1, s2;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    double bbh, survp;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /*extern weight */
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /* We are differentiating ll according to initial status */
 }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
  free_vector(xp,1,npar);    /*for(i=1;i<imx;i++) 
 fclose(ficresprob);      printf(" %d\n",s[4][i]);
     */
 }    cov[1]=1.;
   
 /******************* Printing html file ***********/    for(k=1; k<=nlstate; k++) ll[k]=0.;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  
  int lastpass, int stepm, int weightopt, char model[],\    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\      for(mi=1; mi<= wav[i]-1; mi++){
  char version[], int popforecast ){        for (ii=1;ii<=nlstate+ndeath;ii++)
   int jj1, k1, i1, cpt;          for (j=1;j<=nlstate+ndeath;j++){
   FILE *fichtm;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /*char optionfilehtm[FILENAMELENGTH];*/            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
   strcpy(optionfilehtm,optionfile);        for(d=0; d<dh[mi][i]; d++){
   strcat(optionfilehtm,".htm");          newm=savm;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     printf("Problem with %s \n",optionfilehtm), exit(0);          for (kk=1; kk<=cptcovage;kk++) {
   }            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 \n                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 Total number of observations=%d <br>\n          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
 <hr  size=\"2\" color=\"#EC5E5E\">          savm=oldm;
  <ul><li>Outputs files<br>\n          oldm=newm;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        } /* end mult */
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n        
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        s1=s[mw[mi][i]][i];
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n        s2=s[mw[mi+1][i]][i];
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n        bbh=(double)bh[mi][i]/(double)stepm; 
  - Life expectancies by age and initial health status: <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);        /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
  fprintf(fichtm,"\n         */
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n        if( s2 > nlstate && (mle <5) ){  /* Jackson */
  - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>\n          lli=log(out[s1][s2] - savm[s1][s2]);
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n        } else if  (s2==-2) {
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres);          for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
  if(popforecast==1) fprintf(fichtm,"\n          lli= log(survp);
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n        }else if (mle==1){
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         <br>",fileres,fileres,fileres,fileres);        } else if(mle==2){
  else          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
    fprintf(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);        } else if(mle==3){  /* exponential inter-extrapolation */
 fprintf(fichtm," <li>Graphs</li><p>");          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 */
         } else if (mle==4){  /* mle=4 no inter-extrapolation */
  m=cptcoveff;          lli=log(out[s1][s2]); /* Original formula */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        } else{  /* mle=0 back to 1 */
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
  jj1=0;          /*lli=log(out[s1][s2]); */ /* Original formula */
  for(k1=1; k1<=m;k1++){        } /* End of if */
    for(i1=1; i1<=ncodemax[k1];i1++){        ipmx +=1;
        jj1++;        sw += weight[i];
        if (cptcovn > 0) {        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        /*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 (cpt=1; cpt<=cptcoveff;cpt++)        if(globpr){
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");   %11.6f %11.6f %11.6f ", \
        }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              for(k=1,llt=0.,l=0.; k<=nlstate; k++){
        for(cpt=1; cpt<nlstate;cpt++){            llt +=ll[k]*gipmx/gsw;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          }
        }          fprintf(ficresilk," %10.6f\n", -llt);
     for(cpt=1; cpt<=nlstate;cpt++) {        }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      } /* end of wave */
 interval) in state (%d): v%s%d%d.gif <br>    } /* end of individual */
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      for(cpt=1; cpt<=nlstate;cpt++) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    if(globpr==0){ /* First time we count the contributions and weights */
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      gipmx=ipmx;
      }      gsw=sw;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    }
 health expectancies in states (1) and (2): e%s%d.gif<br>    return -l;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  }
 fprintf(fichtm,"\n</body>");  
    }  
    }  /*************** function likelione ***********/
 fclose(fichtm);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
 }  {
     /* This routine should help understanding what is done with 
 /******************* Gnuplot file **************/       the selection of individuals/waves and
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){       to check the exact contribution to the likelihood.
        Plotting could be done.
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;     */
     int k;
   strcpy(optionfilegnuplot,optionfilefiname);  
   strcat(optionfilegnuplot,".gp.txt");    if(*globpri !=0){ /* Just counts and sums, no printings */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      strcpy(fileresilk,"ilk"); 
     printf("Problem with file %s",optionfilegnuplot);      strcat(fileresilk,fileres);
   }      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
 #ifdef windows        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     fprintf(ficgp,"cd \"%s\" \n",pathc);      }
 #endif      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");
 m=pow(2,cptcoveff);      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]); */
  /* 1eme*/      for(k=1; k<=nlstate; k++) 
   for (cpt=1; cpt<= nlstate ; cpt ++) {        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
    for (k1=1; k1<= m ; k1 ++) {      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
 #ifdef windows  
     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);    *fretone=(*funcone)(p);
 #endif    if(*globpri !=0){
 #ifdef unix      fclose(ficresilk);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
 #endif      fflush(fichtm); 
     } 
 for (i=1; i<= nlstate ; i ++) {    return;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }  
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  /*********** Maximum Likelihood Estimation ***************/
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   else fprintf(ficgp," \%%*lf (\%%*lf)");  {
 }    int i,j, iter;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    double **xi;
      for (i=1; i<= nlstate ; i ++) {    double fret;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double fretone; /* Only one call to likelihood */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /*  char filerespow[FILENAMELENGTH];*/
 }      xi=matrix(1,npar,1,npar);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    for (i=1;i<=npar;i++)
 #ifdef unix      for (j=1;j<=npar;j++)
 fprintf(ficgp,"\nset ter gif small size 400,300");        xi[i][j]=(i==j ? 1.0 : 0.0);
 #endif    printf("Powell\n");  fprintf(ficlog,"Powell\n");
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    strcpy(filerespow,"pow"); 
    }    strcat(filerespow,fileres);
   }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   /*2 eme*/      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   for (k1=1; k1<= m ; k1 ++) {    }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
        for (i=1;i<=nlstate;i++)
     for (i=1; i<= nlstate+1 ; i ++) {      for(j=1;j<=nlstate+ndeath;j++)
       k=2*i;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficrespow,"\n");
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    powell(p,xi,npar,ftol,&iter,&fret,func);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      free_matrix(xi,1,npar,1,npar);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    fclose(ficrespow);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       for (j=1; j<= nlstate+1 ; j ++) {    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
         else fprintf(ficgp," \%%*lf (\%%*lf)");  }
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");  /**** Computes Hessian and covariance matrix ***/
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       for (j=1; j<= nlstate+1 ; j ++) {  {
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double  **a,**y,*x,pd;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double **hess;
 }      int i, j,jk;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    int *indx;
       else fprintf(ficgp,"\" t\"\" w l 0,");  
     }    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   }    void lubksb(double **a, int npar, int *indx, double b[]) ;
      void ludcmp(double **a, int npar, int *indx, double *d) ;
   /*3eme*/    double gompertz(double p[]);
     hess=matrix(1,npar,1,npar);
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<= nlstate ; cpt ++) {    printf("\nCalculation of the hessian matrix. Wait...\n");
       k=2+nlstate*(cpt-1);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       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 (i=1;i<=npar;i++){
       for (i=1; i< nlstate ; i ++) {      printf("%d",i);fflush(stdout);
         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);      fprintf(ficlog,"%d",i);fflush(ficlog);
       }     
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     }      
     }      /*  printf(" %f ",p[i]);
            printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   /* CV preval stat */    }
     for (k1=1; k1<= m ; k1 ++) {    
     for (cpt=1; cpt<nlstate ; cpt ++) {    for (i=1;i<=npar;i++) {
       k=3;      for (j=1;j<=npar;j++)  {
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
       for (i=1; i< nlstate ; i ++)          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         fprintf(ficgp,"+$%d",k+i+1);          hess[i][j]=hessij(p,delti,i,j,func,npar);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          
                hess[j][i]=hess[i][j];    
       l=3+(nlstate+ndeath)*cpt;          /*printf(" %lf ",hess[i][j]);*/
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        }
       for (i=1; i< nlstate ; i ++) {      }
         l=3+(nlstate+ndeath)*cpt;    }
         fprintf(ficgp,"+$%d",l+i+1);    printf("\n");
       }    fprintf(ficlog,"\n");
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   }      
      a=matrix(1,npar,1,npar);
   /* proba elementaires */    y=matrix(1,npar,1,npar);
    for(i=1,jk=1; i <=nlstate; i++){    x=vector(1,npar);
     for(k=1; k <=(nlstate+ndeath); k++){    indx=ivector(1,npar);
       if (k != i) {    for (i=1;i<=npar;i++)
         for(j=1; j <=ncovmodel; j++){      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
            ludcmp(a,npar,indx,&pd);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  
           jk++;    for (j=1;j<=npar;j++) {
           fprintf(ficgp,"\n");      for (i=1;i<=npar;i++) x[i]=0;
         }      x[j]=1;
       }      lubksb(a,npar,indx,x);
     }      for (i=1;i<=npar;i++){ 
     }        matcov[i][j]=x[i];
       }
     for(jk=1; jk <=m; jk++) {    }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);  
    i=1;    printf("\n#Hessian matrix#\n");
    for(k2=1; k2<=nlstate; k2++) {    fprintf(ficlog,"\n#Hessian matrix#\n");
      k3=i;    for (i=1;i<=npar;i++) { 
      for(k=1; k<=(nlstate+ndeath); k++) {      for (j=1;j<=npar;j++) { 
        if (k != k2){        printf("%.3e ",hess[i][j]);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        fprintf(ficlog,"%.3e ",hess[i][j]);
 ij=1;      }
         for(j=3; j <=ncovmodel; j++) {      printf("\n");
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      fprintf(ficlog,"\n");
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    }
             ij++;  
           }    /* Recompute Inverse */
           else    for (i=1;i<=npar;i++)
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         }    ludcmp(a,npar,indx,&pd);
           fprintf(ficgp,")/(1");  
            /*  printf("\n#Hessian matrix recomputed#\n");
         for(k1=1; k1 <=nlstate; k1++){    
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    for (j=1;j<=npar;j++) {
 ij=1;      for (i=1;i<=npar;i++) x[i]=0;
           for(j=3; j <=ncovmodel; j++){      x[j]=1;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      lubksb(a,npar,indx,x);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      for (i=1;i<=npar;i++){ 
             ij++;        y[i][j]=x[i];
           }        printf("%.3e ",y[i][j]);
           else        fprintf(ficlog,"%.3e ",y[i][j]);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      }
           }      printf("\n");
           fprintf(ficgp,")");      fprintf(ficlog,"\n");
         }    }
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  
         i=i+ncovmodel;    free_matrix(a,1,npar,1,npar);
        }    free_matrix(y,1,npar,1,npar);
      }    free_vector(x,1,npar);
    }    free_ivector(indx,1,npar);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    free_matrix(hess,1,npar,1,npar);
    }  
      
   fclose(ficgp);  }
 }  /* end gnuplot */  
   /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 /*************** Moving average **************/  {
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    int i;
     int l=1, lmax=20;
   int i, cpt, cptcod;    double k1,k2;
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    double p2[MAXPARM+1]; /* identical to x */
       for (i=1; i<=nlstate;i++)    double res;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           mobaverage[(int)agedeb][i][cptcod]=0.;    double fx;
        int k=0,kmax=10;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    double l1;
       for (i=1; i<=nlstate;i++){  
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fx=func(x);
           for (cpt=0;cpt<=4;cpt++){    for (i=1;i<=npar;i++) p2[i]=x[i];
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
           }      l1=pow(10,l);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      delts=delt;
         }      for(k=1 ; k <kmax; k=k+1){
       }        delt = delta*(l1*k);
     }        p2[theta]=x[theta] +delt;
            k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
 }        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
 /************** Forecasting ******************/        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 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 DEBUGHESS
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        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);
   int *popage;        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);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  #endif
   double *popeffectif,*popcount;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   double ***p3mat;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   char fileresf[FILENAMELENGTH];          k=kmax;
         }
  agelim=AGESUP;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          k=kmax; l=lmax*10.;
         }
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
            delts=delt;
          }
   strcpy(fileresf,"f");      }
   strcat(fileresf,fileres);    }
   if((ficresf=fopen(fileresf,"w"))==NULL) {    delti[theta]=delts;
     printf("Problem with forecast resultfile: %s\n", fileresf);    return res; 
   }    
   printf("Computing forecasting: result on file '%s' \n", fileresf);  }
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   {
   if (mobilav==1) {    int i;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int l=1, l1, lmax=20;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    double k1,k2,k3,k4,res,fx;
   }    double p2[MAXPARM+1];
     int k;
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;    fx=func(x);
      for (k=1; k<=2; k++) {
   agelim=AGESUP;      for (i=1;i<=npar;i++) p2[i]=x[i];
        p2[thetai]=x[thetai]+delti[thetai]/k;
   hstepm=1;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   hstepm=hstepm/stepm;      k1=func(p2)-fx;
   yp1=modf(dateintmean,&yp);    
   anprojmean=yp;      p2[thetai]=x[thetai]+delti[thetai]/k;
   yp2=modf((yp1*12),&yp);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   mprojmean=yp;      k2=func(p2)-fx;
   yp1=modf((yp2*30.5),&yp);    
   jprojmean=yp;      p2[thetai]=x[thetai]-delti[thetai]/k;
   if(jprojmean==0) jprojmean=1;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   if(mprojmean==0) jprojmean=1;      k3=func(p2)-fx;
      
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      p2[thetai]=x[thetai]-delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   for(cptcov=1;cptcov<=i2;cptcov++){      k4=func(p2)-fx;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       k=k+1;  #ifdef DEBUG
       fprintf(ficresf,"\n#******");      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);
       for(j=1;j<=cptcoveff;j++) {      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);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  #endif
       }    }
       fprintf(ficresf,"******\n");    return res;
       fprintf(ficresf,"# StartingAge FinalAge");  }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  
        /************** Inverse of matrix **************/
        void ludcmp(double **a, int n, int *indx, double *d) 
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  { 
         fprintf(ficresf,"\n");    int i,imax,j,k; 
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      double big,dum,sum,temp; 
     double *vv; 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){   
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    vv=vector(1,n); 
           nhstepm = nhstepm/hstepm;    *d=1.0; 
              for (i=1;i<=n;i++) { 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      big=0.0; 
           oldm=oldms;savm=savms;      for (j=1;j<=n;j++) 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          if ((temp=fabs(a[i][j])) > big) big=temp; 
              if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           for (h=0; h<=nhstepm; h++){      vv[i]=1.0/big; 
             if (h==(int) (calagedate+YEARM*cpt)) {    } 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    for (j=1;j<=n;j++) { 
             }      for (i=1;i<j;i++) { 
             for(j=1; j<=nlstate+ndeath;j++) {        sum=a[i][j]; 
               kk1=0.;kk2=0;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
               for(i=1; i<=nlstate;i++) {                      a[i][j]=sum; 
                 if (mobilav==1)      } 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      big=0.0; 
                 else {      for (i=j;i<=n;i++) { 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        sum=a[i][j]; 
                 }        for (k=1;k<j;k++) 
                          sum -= a[i][k]*a[k][j]; 
               }        a[i][j]=sum; 
               if (h==(int)(calagedate+12*cpt)){        if ( (dum=vv[i]*fabs(sum)) >= big) { 
                 fprintf(ficresf," %.3f", kk1);          big=dum; 
                                  imax=i; 
               }        } 
             }      } 
           }      if (j != imax) { 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (k=1;k<=n;k++) { 
         }          dum=a[imax][k]; 
       }          a[imax][k]=a[j][k]; 
     }          a[j][k]=dum; 
   }        } 
                *d = -(*d); 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        vv[imax]=vv[j]; 
       } 
   fclose(ficresf);      indx[j]=imax; 
 }      if (a[j][j] == 0.0) a[j][j]=TINY; 
 /************** Forecasting ******************/      if (j != n) { 
 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){        dum=1.0/(a[j][j]); 
          for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      } 
   int *popage;    } 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    free_vector(vv,1,n);  /* Doesn't work */
   double *popeffectif,*popcount;  ;
   double ***p3mat,***tabpop,***tabpopprev;  } 
   char filerespop[FILENAMELENGTH];  
   void lubksb(double **a, int n, int *indx, double b[]) 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  { 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int i,ii=0,ip,j; 
   agelim=AGESUP;    double sum; 
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;   
      for (i=1;i<=n;i++) { 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      ip=indx[i]; 
        sum=b[ip]; 
        b[ip]=b[i]; 
   strcpy(filerespop,"pop");      if (ii) 
   strcat(filerespop,fileres);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      else if (sum) ii=i; 
     printf("Problem with forecast resultfile: %s\n", filerespop);      b[i]=sum; 
   }    } 
   printf("Computing forecasting: result on file '%s' \n", filerespop);    for (i=n;i>=1;i--) { 
       sum=b[i]; 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
   if (mobilav==1) {    } 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  } 
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }  void pstamp(FILE *fichier)
   {
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   if (stepm<=12) stepsize=1;  }
    
   agelim=AGESUP;  /************ Frequencies ********************/
    void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
   hstepm=1;  {  /* Some frequencies */
   hstepm=hstepm/stepm;    
      int i, m, jk, k1,i1, j1, bool, z1,j;
   if (popforecast==1) {    int first;
     if((ficpop=fopen(popfile,"r"))==NULL) {    double ***freq; /* Frequencies */
       printf("Problem with population file : %s\n",popfile);exit(0);    double *pp, **prop;
     }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     popage=ivector(0,AGESUP);    char fileresp[FILENAMELENGTH];
     popeffectif=vector(0,AGESUP);    
     popcount=vector(0,AGESUP);    pp=vector(1,nlstate);
        prop=matrix(1,nlstate,iagemin,iagemax+3);
     i=1;      strcpy(fileresp,"p");
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    strcat(fileresp,fileres);
        if((ficresp=fopen(fileresp,"w"))==NULL) {
     imx=i;      printf("Problem with prevalence resultfile: %s\n", fileresp);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   }      exit(0);
     }
   for(cptcov=1;cptcov<=i2;cptcov++){    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    j1=0;
       k=k+1;    
       fprintf(ficrespop,"\n#******");    j=cptcoveff;
       for(j=1;j<=cptcoveff;j++) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }    first=1;
       fprintf(ficrespop,"******\n");  
       fprintf(ficrespop,"# Age");    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
       if (popforecast==1)  fprintf(ficrespop," [Population]");    /*    j1++;
        */
       for (cpt=0; cpt<=0;cpt++) {    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                  scanf("%d", i);*/
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for (i=-5; i<=nlstate+ndeath; i++)  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
           nhstepm = nhstepm/hstepm;            for(m=iagemin; m <= iagemax+3; m++)
                        freq[i][jk][m]=0;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        
           oldm=oldms;savm=savms;        for (i=1; i<=nlstate; i++)  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for(m=iagemin; m <= iagemax+3; m++)
                    prop[i][m]=0;
           for (h=0; h<=nhstepm; h++){        
             if (h==(int) (calagedate+YEARM*cpt)) {        dateintsum=0;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        k2cpt=0;
             }        for (i=1; i<=imx; i++) {
             for(j=1; j<=nlstate+ndeath;j++) {          bool=1;
               kk1=0.;kk2=0;          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
               for(i=1; i<=nlstate;i++) {                          for (z1=1; z1<=cptcoveff; z1++)       
                 if (mobilav==1)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
                 else {                bool=0;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
                 }                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
               }                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
               if (h==(int)(calagedate+12*cpt)){                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;              } 
                   /*fprintf(ficrespop," %.3f", kk1);          }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/   
               }          if (bool==1){
             }            for(m=firstpass; m<=lastpass; m++){
             for(i=1; i<=nlstate;i++){              k2=anint[m][i]+(mint[m][i]/12.);
               kk1=0.;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                 for(j=1; j<=nlstate;j++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];                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];
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];                if (m<lastpass) {
             }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)                }
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);                
           }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                  dateintsum=dateintsum+k2;
         }                  k2cpt++;
       }                }
                  /*}*/
   /******/            }
           }
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        } /* end i */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);           
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        pstamp(ficresp);
           nhstepm = nhstepm/hstepm;        if  (cptcovn>0) {
                    fprintf(ficresp, "\n#********** Variable "); 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           oldm=oldms;savm=savms;          fprintf(ficresp, "**********\n#");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            fprintf(ficlog, "\n#********** Variable "); 
           for (h=0; h<=nhstepm; h++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             if (h==(int) (calagedate+YEARM*cpt)) {          fprintf(ficlog, "**********\n#");
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        }
             }        for(i=1; i<=nlstate;i++) 
             for(j=1; j<=nlstate+ndeath;j++) {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
               kk1=0.;kk2=0;        fprintf(ficresp, "\n");
               for(i=1; i<=nlstate;i++) {                      
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            for(i=iagemin; i <= iagemax+3; i++){
               }          if(i==iagemax+3){
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);            fprintf(ficlog,"Total");
             }          }else{
           }            if(first==1){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              first=0;
         }              printf("See log file for details...\n");
       }            }
    }            fprintf(ficlog,"Age %d", i);
   }          }
            for(jk=1; jk <=nlstate ; jk++){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
   if (popforecast==1) {          }
     free_ivector(popage,0,AGESUP);          for(jk=1; jk <=nlstate ; jk++){
     free_vector(popeffectif,0,AGESUP);            for(m=-1, pos=0; m <=0 ; m++)
     free_vector(popcount,0,AGESUP);              pos += freq[jk][m][i];
   }            if(pp[jk]>=1.e-10){
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              if(first==1){
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   fclose(ficrespop);              }
 }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
 /***********************************************/              if(first==1)
 /**************** Main Program *****************/                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 /***********************************************/              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
 int main(int argc, char *argv[])          }
 {  
           for(jk=1; jk <=nlstate ; jk++){
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   double agedeb, agefin,hf;              pp[jk] += freq[jk][m][i];
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   double fret;            pos += pp[jk];
   double **xi,tmp,delta;            posprop += prop[jk][i];
           }
   double dum; /* Dummy variable */          for(jk=1; jk <=nlstate ; jk++){
   double ***p3mat;            if(pos>=1.e-5){
   int *indx;              if(first==1)
   char line[MAXLINE], linepar[MAXLINE];                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   char title[MAXLINE];              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];            }else{
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];              if(first==1)
                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
   char filerest[FILENAMELENGTH];            if( i <= iagemax){
   char fileregp[FILENAMELENGTH];              if(pos>=1.e-5){
   char popfile[FILENAMELENGTH];                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                /*probs[i][jk][j1]= pp[jk]/pos;*/
   int firstobs=1, lastobs=10;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   int sdeb, sfin; /* Status at beginning and end */              }
   int c,  h , cpt,l;              else
   int ju,jl, mi;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          }
   int mobilav=0,popforecast=0;          
   int hstepm, nhstepm;          for(jk=-1; jk <=nlstate+ndeath; jk++)
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
   double bage, fage, age, agelim, agebase;              if(first==1)
   double ftolpl=FTOL;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   double **prlim;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   double *severity;              }
   double ***param; /* Matrix of parameters */          if(i <= iagemax)
   double  *p;            fprintf(ficresp,"\n");
   double **matcov; /* Matrix of covariance */          if(first==1)
   double ***delti3; /* Scale */            printf("Others in log...\n");
   double *delti; /* Scale */          fprintf(ficlog,"\n");
   double ***eij, ***vareij;        }
   double **varpl; /* Variances of prevalence limits by age */        /*}*/
   double *epj, vepp;    }
   double kk1, kk2;    dateintmean=dateintsum/k2cpt; 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;   
      fclose(ficresp);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";    free_vector(pp,1,nlstate);
   char *alph[]={"a","a","b","c","d","e"}, str[4];    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
   }
   char z[1]="c", occ;  
 #include <sys/time.h>  /************ Prevalence ********************/
 #include <time.h>  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  {  
      /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   /* long total_usecs;       in each health status at the date of interview (if between dateprev1 and dateprev2).
   struct timeval start_time, end_time;       We still use firstpass and lastpass as another selection.
      */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */   
   getcwd(pathcd, size);    int i, m, jk, k1, i1, j1, bool, z1,j;
     double ***freq; /* Frequencies */
   printf("\n%s",version);    double *pp, **prop;
   if(argc <=1){    double pos,posprop; 
     printf("\nEnter the parameter file name: ");    double  y2; /* in fractional years */
     scanf("%s",pathtot);    int iagemin, iagemax;
   }    int first; /** to stop verbosity which is redirected to log file */
   else{  
     strcpy(pathtot,argv[1]);    iagemin= (int) agemin;
   }    iagemax= (int) agemax;
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    /*pp=vector(1,nlstate);*/
   /*cygwin_split_path(pathtot,path,optionfile);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   /* cutv(path,optionfile,pathtot,'\\');*/    j1=0;
     
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    /*j=cptcoveff;*/
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   chdir(path);    
   replace(pathc,path);    first=1;
     for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
 /*-------- arguments in the command line --------*/      /*for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;*/
   strcpy(fileres,"r");        
   strcat(fileres, optionfilefiname);        for (i=1; i<=nlstate; i++)  
   strcat(fileres,".txt");    /* Other files have txt extension */          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
   /*---------arguments file --------*/       
         for (i=1; i<=imx; i++) { /* Each individual */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          bool=1;
     printf("Problem with optionfile %s\n",optionfile);          if  (cptcovn>0) {
     goto end;            for (z1=1; z1<=cptcoveff; z1++) 
   }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
   strcpy(filereso,"o");          } 
   strcat(filereso,fileres);          if (bool==1) { 
   if((ficparo=fopen(filereso,"w"))==NULL) {            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     printf("Problem with Output resultfile: %s\n", filereso);goto end;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
   /* Reads comments: lines beginning with '#' */                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   while((c=getc(ficpar))=='#' && c!= EOF){                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); 
     ungetc(c,ficpar);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     fgets(line, MAXLINE, ficpar);                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
     puts(line);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     fputs(line,ficparo);                  prop[s[m][i]][iagemax+3] += weight[i]; 
   }                } 
   ungetc(c,ficpar);              }
             } /* end selection of waves */
   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);          }
   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);        for(i=iagemin; i <= iagemax+3; i++){  
 while((c=getc(ficpar))=='#' && c!= EOF){          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     ungetc(c,ficpar);            posprop += prop[jk][i]; 
     fgets(line, MAXLINE, ficpar);          } 
     puts(line);          
     fputs(line,ficparo);          for(jk=1; jk <=nlstate ; jk++){     
   }            if( i <=  iagemax){ 
   ungetc(c,ficpar);              if(posprop>=1.e-5){ 
                  probs[i][jk][j1]= prop[jk][i]/posprop;
                  } else{
   covar=matrix(0,NCOVMAX,1,n);                if(first==1){
   cptcovn=0;                  first=0;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                  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]);
                 }
   ncovmodel=2+cptcovn;              }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */            } 
            }/* end jk */ 
   /* Read guess parameters */        }/* end i */ 
   /* Reads comments: lines beginning with '#' */      /*} *//* end i1 */
   while((c=getc(ficpar))=='#' && c!= EOF){    } /* end j1 */
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     puts(line);    /*free_vector(pp,1,nlstate);*/
     fputs(line,ficparo);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  }  /* End of prevalence */
   ungetc(c,ficpar);  
    /************* Waves Concatenation ***************/
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
     for(j=1; j <=nlstate+ndeath-1; j++){  {
       fscanf(ficpar,"%1d%1d",&i1,&j1);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       fprintf(ficparo,"%1d%1d",i1,j1);       Death is a valid wave (if date is known).
       printf("%1d%1d",i,j);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       for(k=1; k<=ncovmodel;k++){       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         fscanf(ficpar," %lf",&param[i][j][k]);       and mw[mi+1][i]. dh depends on stepm.
         printf(" %lf",param[i][j][k]);       */
         fprintf(ficparo," %lf",param[i][j][k]);  
       }    int i, mi, m;
       fscanf(ficpar,"\n");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       printf("\n");       double sum=0., jmean=0.;*/
       fprintf(ficparo,"\n");    int first;
     }    int j, k=0,jk, ju, jl;
      double sum=0.;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    first=0;
     jmin=1e+5;
   p=param[1][1];    jmax=-1;
      jmean=0.;
   /* Reads comments: lines beginning with '#' */    for(i=1; i<=imx; i++){
   while((c=getc(ficpar))=='#' && c!= EOF){      mi=0;
     ungetc(c,ficpar);      m=firstpass;
     fgets(line, MAXLINE, ficpar);      while(s[m][i] <= nlstate){
     puts(line);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     fputs(line,ficparo);          mw[++mi][i]=m;
   }        if(m >=lastpass)
   ungetc(c,ficpar);          break;
         else
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          m++;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      }/* end while */
   for(i=1; i <=nlstate; i++){      if (s[m][i] > nlstate){
     for(j=1; j <=nlstate+ndeath-1; j++){        mi++;     /* Death is another wave */
       fscanf(ficpar,"%1d%1d",&i1,&j1);        /* if(mi==0)  never been interviewed correctly before death */
       printf("%1d%1d",i,j);           /* Only death is a correct wave */
       fprintf(ficparo,"%1d%1d",i1,j1);        mw[mi][i]=m;
       for(k=1; k<=ncovmodel;k++){      }
         fscanf(ficpar,"%le",&delti3[i][j][k]);  
         printf(" %le",delti3[i][j][k]);      wav[i]=mi;
         fprintf(ficparo," %le",delti3[i][j][k]);      if(mi==0){
       }        nbwarn++;
       fscanf(ficpar,"\n");        if(first==0){
       printf("\n");          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       fprintf(ficparo,"\n");          first=1;
     }        }
   }        if(first==1){
   delti=delti3[1][1];          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
          }
   /* Reads comments: lines beginning with '#' */      } /* end mi==0 */
   while((c=getc(ficpar))=='#' && c!= EOF){    } /* End individuals */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    for(i=1; i<=imx; i++){
     puts(line);      for(mi=1; mi<wav[i];mi++){
     fputs(line,ficparo);        if (stepm <=0)
   }          dh[mi][i]=1;
   ungetc(c,ficpar);        else{
            if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   matcov=matrix(1,npar,1,npar);            if (agedc[i] < 2*AGESUP) {
   for(i=1; i <=npar; i++){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     fscanf(ficpar,"%s",&str);              if(j==0) j=1;  /* Survives at least one month after exam */
     printf("%s",str);              else if(j<0){
     fprintf(ficparo,"%s",str);                nberr++;
     for(j=1; j <=i; j++){                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fscanf(ficpar," %le",&matcov[i][j]);                j=1; /* Temporary Dangerous patch */
       printf(" %.5le",matcov[i][j]);                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);
       fprintf(ficparo," %.5le",matcov[i][j]);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
     fscanf(ficpar,"\n");              }
     printf("\n");              k=k+1;
     fprintf(ficparo,"\n");              if (j >= jmax){
   }                jmax=j;
   for(i=1; i <=npar; i++)                ijmax=i;
     for(j=i+1;j<=npar;j++)              }
       matcov[i][j]=matcov[j][i];              if (j <= jmin){
                    jmin=j;
   printf("\n");                ijmin=i;
               }
               sum=sum+j;
     /*-------- Rewriting paramater file ----------*/              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
      strcpy(rfileres,"r");    /* "Rparameterfile */              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/            }
      strcat(rfileres,".");    /* */          }
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          else{
     if((ficres =fopen(rfileres,"w"))==NULL) {            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       printf("Problem writing new parameter file: %s\n", fileres);goto end;  /*        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]); */
     }  
     fprintf(ficres,"#%s\n",version);            k=k+1;
                if (j >= jmax) {
     /*-------- data file ----------*/              jmax=j;
     if((fic=fopen(datafile,"r"))==NULL)    {              ijmax=i;
       printf("Problem with datafile: %s\n", datafile);goto end;            }
     }            else if (j <= jmin){
               jmin=j;
     n= lastobs;              ijmin=i;
     severity = vector(1,maxwav);            }
     outcome=imatrix(1,maxwav+1,1,n);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     num=ivector(1,n);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
     moisnais=vector(1,n);            if(j<0){
     annais=vector(1,n);              nberr++;
     moisdc=vector(1,n);              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]);
     andc=vector(1,n);              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]);
     agedc=vector(1,n);            }
     cod=ivector(1,n);            sum=sum+j;
     weight=vector(1,n);          }
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          jk= j/stepm;
     mint=matrix(1,maxwav,1,n);          jl= j -jk*stepm;
     anint=matrix(1,maxwav,1,n);          ju= j -(jk+1)*stepm;
     s=imatrix(1,maxwav+1,1,n);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     adl=imatrix(1,maxwav+1,1,n);                if(jl==0){
     tab=ivector(1,NCOVMAX);              dh[mi][i]=jk;
     ncodemax=ivector(1,8);              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
     i=1;                    * to avoid the price of an extra matrix product in likelihood */
     while (fgets(line, MAXLINE, fic) != NULL)    {              dh[mi][i]=jk+1;
       if ((i >= firstobs) && (i <=lastobs)) {              bh[mi][i]=ju;
                    }
         for (j=maxwav;j>=1;j--){          }else{
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            if(jl <= -ju){
           strcpy(line,stra);              dh[mi][i]=jk;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=jl;       /* bias is positive if real duration
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                                   * is higher than the multiple of stepm and negative otherwise.
         }                                   */
                    }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            else{
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=ju; /* At least one step */
         for (j=ncovcol;j>=1;j--){              /*  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);*/
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            }
         }          } /* end if mle */
         num[i]=atol(stra);        }
              } /* end wave */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    }
           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;}*/    jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
         i=i+1;    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("ii=%d", ij);  /*********** Tricode ****************************/
        scanf("%d",i);*/  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   imx=i-1; /* Number of individuals */  {
     /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   /* for (i=1; i<=imx; i++){    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    /* nbcode[Tvar[j]][1]= 
     }*/    */
    
   /* for (i=1; i<=imx; i++){    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
      if (s[4][i]==9)  s[4][i]=-1;    int modmaxcovj=0; /* Modality max of covariates j */
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}    int cptcode=0; /* Modality max of covariates j */
   */    int modmincovj=0; /* Modality min of covariates j */
    
   /* Calculation of the number of parameter from char model*/  
   Tvar=ivector(1,15);    cptcoveff=0; 
   Tprod=ivector(1,15);   
   Tvaraff=ivector(1,15);    for (k=-1; k < maxncov; k++) Ndum[k]=0;
   Tvard=imatrix(1,15,1,2);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   Tage=ivector(1,15);        
        /* Loop on covariates without age and products */
   if (strlen(model) >1){    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
     j=0, j1=0, k1=1, k2=1;      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
     j=nbocc(model,'+');                                 modality of this covariate Vj*/ 
     j1=nbocc(model,'*');        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
     cptcovn=j+1;                                      * If product of Vn*Vm, still boolean *:
     cptcovprod=j1;                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                                          * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
     strcpy(modelsav,model);        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){                                        modality of the nth covariate of individual i. */
       printf("Error. Non available option model=%s ",model);        if (ij > modmaxcovj)
       goto end;          modmaxcovj=ij; 
     }        else if (ij < modmincovj) 
              modmincovj=ij; 
     for(i=(j+1); i>=1;i--){        if ((ij < -1) && (ij > NCOVMAX)){
       cutv(stra,strb,modelsav,'+');          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);          exit(1);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        }else
       /*scanf("%d",i);*/        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
       if (strchr(strb,'*')) {        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
         cutv(strd,strc,strb,'*');        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if (strcmp(strc,"age")==0) {        /* getting the maximum value of the modality of the covariate
           cptcovprod--;           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
           cutv(strb,stre,strd,'V');           female is 1, then modmaxcovj=1.*/
           Tvar[i]=atoi(stre);      }
           cptcovage++;      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
             Tage[cptcovage]=i;      cptcode=modmaxcovj;
             /*printf("stre=%s ", stre);*/      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
         }     /*for (i=0; i<=cptcode; i++) {*/
         else if (strcmp(strd,"age")==0) {      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
           cptcovprod--;        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
           cutv(strb,stre,strc,'V');        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           Tvar[i]=atoi(stre);          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
           cptcovage++;        }
           Tage[cptcovage]=i;        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
         }           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
         else {      } /* Ndum[-1] number of undefined modalities */
           cutv(strb,stre,strc,'V');  
           Tvar[i]=ncovcol+k1;      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
           cutv(strb,strc,strd,'V');      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
           Tprod[k1]=i;      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
           Tvard[k1][1]=atoi(strc);         modmincovj=3; modmaxcovj = 7;
           Tvard[k1][2]=atoi(stre);         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
           Tvar[cptcovn+k2]=Tvard[k1][1];         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];         variables V1_1 and V1_2.
           for (k=1; k<=lastobs;k++)         nbcode[Tvar[j]][ij]=k;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];         nbcode[Tvar[j]][1]=0;
           k1++;         nbcode[Tvar[j]][2]=1;
           k2=k2+2;         nbcode[Tvar[j]][3]=2;
         }      */
       }      ij=1; /* ij is similar to i but can jumps over null modalities */
       else {      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
        /*  scanf("%d",i);*/          /*recode from 0 */
       cutv(strd,strc,strb,'V');          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
       Tvar[i]=atoi(strc);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
       }                                       k is a modality. If we have model=V1+V1*sex 
       strcpy(modelsav,stra);                                         then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);            ij++;
         scanf("%d",i);*/          }
     }          if (ij > ncodemax[j]) break; 
 }        }  /* end of loop on */
        } /* end of loop on modality */ 
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   printf("cptcovprod=%d ", cptcovprod);    
   scanf("%d ",i);*/   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     fclose(fic);    
     for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
     /*  if(mle==1){*/     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
     if (weightopt != 1) { /* Maximisation without weights*/     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
       for(i=1;i<=n;i++) weight[i]=1.0;     Ndum[ij]++; 
     }   } 
     /*-calculation of age at interview from date of interview and age at death -*/  
     agev=matrix(1,maxwav,1,imx);   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) */
     for (i=1; i<=imx; i++) {     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
       for(m=2; (m<= maxwav); m++) {     if((Ndum[i]!=0) && (i<=ncovcol)){
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
          anint[m][i]=9999;       Tvaraff[ij]=i; /*For printing (unclear) */
          s[m][i]=-1;       ij++;
        }     }else
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;         Tvaraff[ij]=0;
       }   }
     }   ij--;
    cptcoveff=ij; /*Number of total covariates*/
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  }
       for(m=1; (m<= maxwav); m++){  
         if(s[m][i] >0){  
           if (s[m][i] >= nlstate+1) {  /*********** Health Expectancies ****************/
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
                 agev[m][i]=agedc[i];  
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  {
            else {    /* Health expectancies, no variances */
               if (andc[i]!=9999){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    int nhstepma, nstepma; /* Decreasing with age */
               agev[m][i]=-1;    double age, agelim, hf;
               }    double ***p3mat;
             }    double eip;
           }  
           else if(s[m][i] !=9){ /* Should no more exist */    pstamp(ficreseij);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
             if(mint[m][i]==99 || anint[m][i]==9999)    fprintf(ficreseij,"# Age");
               agev[m][i]=1;    for(i=1; i<=nlstate;i++){
             else if(agev[m][i] <agemin){      for(j=1; j<=nlstate;j++){
               agemin=agev[m][i];        fprintf(ficreseij," e%1d%1d ",i,j);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      }
             }      fprintf(ficreseij," e%1d. ",i);
             else if(agev[m][i] >agemax){    }
               agemax=agev[m][i];    fprintf(ficreseij,"\n");
              /* 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];*/    if(estepm < stepm){
             /*   agev[m][i] = age[i]+2*m;*/      printf ("Problem %d lower than %d\n",estepm, stepm);
           }    }
           else { /* =9 */    else  hstepm=estepm;   
             agev[m][i]=1;    /* We compute the life expectancy from trapezoids spaced every estepm months
             s[m][i]=-1;     * This is mainly to measure the difference between two models: for example
           }     * if stepm=24 months pijx are given only every 2 years and by summing them
         }     * we are calculating an estimate of the Life Expectancy assuming a linear 
         else /*= 0 Unknown */     * progression in between and thus overestimating or underestimating according
           agev[m][i]=1;     * to the curvature of the survival function. If, for the same date, we 
       }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         * to compare the new estimate of Life expectancy with the same linear 
     }     * hypothesis. A more precise result, taking into account a more precise
     for (i=1; i<=imx; i++)  {     * curvature will be obtained if estepm is as small as stepm. */
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {    /* For example we decided to compute the life expectancy with the smallest unit */
           printf("Error: Wrong value in nlstate or ndeath\n");      /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           goto end;       nhstepm is the number of hstepm from age to agelim 
         }       nstepm is the number of stepm from age to agelin. 
       }       Look at hpijx to understand the reason of that which relies in memory size
     }       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);       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
     free_vector(severity,1,maxwav);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     free_imatrix(outcome,1,maxwav+1,1,n);       results. So we changed our mind and took the option of the best precision.
     free_vector(moisnais,1,n);    */
     free_vector(annais,1,n);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/    agelim=AGESUP;
     free_vector(moisdc,1,n);    /* If stepm=6 months */
     free_vector(andc,1,n);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
          
     wav=ivector(1,imx);  /* nhstepm age range expressed in number of stepm */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        /* if (stepm >= YEARM) hstepm=1;*/
     /* Concatenates waves */    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
     for (age=bage; age<=fage; age ++){ 
       Tcode=ivector(1,100);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       ncodemax[1]=1;      /* if (stepm >= YEARM) hstepm=1;*/
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
        
    codtab=imatrix(1,100,1,10);      /* If stepm=6 months */
    h=0;      /* Computed by stepm unit matrices, product of hstepma matrices, stored
    m=pow(2,cptcoveff);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
        
    for(k=1;k<=cptcoveff; k++){      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
      for(i=1; i <=(m/pow(2,k));i++){      
        for(j=1; j <= ncodemax[k]; j++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      
            h++;      printf("%d|",(int)age);fflush(stdout);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/      
          }      /* Computing expectancies */
        }      for(i=1; i<=nlstate;i++)
      }        for(j=1; j<=nlstate;j++)
    }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       codtab[1][2]=1;codtab[2][2]=2; */            
    /* for(i=1; i <=m ;i++){            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       for(k=1; k <=cptcovn; k++){  
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);          }
       }  
       printf("\n");      fprintf(ficreseij,"%3.0f",age );
       }      for(i=1; i<=nlstate;i++){
       scanf("%d",i);*/        eip=0;
            for(j=1; j<=nlstate;j++){
    /* Calculates basic frequencies. Computes observed prevalence at single age          eip +=eij[i][j][(int)age];
        and prints on file fileres'p'. */          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
            fprintf(ficreseij,"%9.4f", eip );
          }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficreseij,"\n");
     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 */    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    printf("\n");
          fprintf(ficlog,"\n");
     /* 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) */  
   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[] )
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  {
     }    /* Covariances of health expectancies eij and of total life expectancies according
         to initial status i, ei. .
     /*--------- 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);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
      int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
    jk=1;    double ***p3matp, ***p3matm, ***varhe;
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    double **dnewm,**doldm;
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    double *xp, *xm;
    for(i=1,jk=1; i <=nlstate; i++){    double **gp, **gm;
      for(k=1; k <=(nlstate+ndeath); k++){    double ***gradg, ***trgradg;
        if (k != i)    int theta;
          {  
            printf("%d%d ",i,k);    double eip, vip;
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
              printf("%f ",p[jk]);    xp=vector(1,npar);
              fprintf(ficres,"%f ",p[jk]);    xm=vector(1,npar);
              jk++;    dnewm=matrix(1,nlstate*nlstate,1,npar);
            }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
            printf("\n");    
            fprintf(ficres,"\n");    pstamp(ficresstdeij);
          }    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
      }    fprintf(ficresstdeij,"# Age");
    }    for(i=1; i<=nlstate;i++){
  if(mle==1){      for(j=1; j<=nlstate;j++)
     /* Computing hessian and covariance matrix */        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
     ftolhess=ftol; /* Usually correct */      fprintf(ficresstdeij," e%1d. ",i);
     hesscov(matcov, p, npar, delti, ftolhess, func);    }
  }    fprintf(ficresstdeij,"\n");
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");  
     printf("# Scales (for hessian or gradient estimation)\n");    pstamp(ficrescveij);
      for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
       for(j=1; j <=nlstate+ndeath; j++){    fprintf(ficrescveij,"# Age");
         if (j!=i) {    for(i=1; i<=nlstate;i++)
           fprintf(ficres,"%1d%1d",i,j);      for(j=1; j<=nlstate;j++){
           printf("%1d%1d",i,j);        cptj= (j-1)*nlstate+i;
           for(k=1; k<=ncovmodel;k++){        for(i2=1; i2<=nlstate;i2++)
             printf(" %.5e",delti[jk]);          for(j2=1; j2<=nlstate;j2++){
             fprintf(ficres," %.5e",delti[jk]);            cptj2= (j2-1)*nlstate+i2;
             jk++;            if(cptj2 <= cptj)
           }              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           printf("\n");          }
           fprintf(ficres,"\n");      }
         }    fprintf(ficrescveij,"\n");
       }    
      }    if(estepm < stepm){
          printf ("Problem %d lower than %d\n",estepm, stepm);
     k=1;    }
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    else  hstepm=estepm;   
     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");    /* We compute the life expectancy from trapezoids spaced every estepm months
     for(i=1;i<=npar;i++){     * This is mainly to measure the difference between two models: for example
       /*  if (k>nlstate) k=1;     * if stepm=24 months pijx are given only every 2 years and by summing them
       i1=(i-1)/(ncovmodel*nlstate)+1;     * we are calculating an estimate of the Life Expectancy assuming a linear 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);     * progression in between and thus overestimating or underestimating according
       printf("%s%d%d",alph[k],i1,tab[i]);*/     * to the curvature of the survival function. If, for the same date, we 
       fprintf(ficres,"%3d",i);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       printf("%3d",i);     * to compare the new estimate of Life expectancy with the same linear 
       for(j=1; j<=i;j++){     * hypothesis. A more precise result, taking into account a more precise
         fprintf(ficres," %.5e",matcov[i][j]);     * curvature will be obtained if estepm is as small as stepm. */
         printf(" %.5e",matcov[i][j]);  
       }    /* For example we decided to compute the life expectancy with the smallest unit */
       fprintf(ficres,"\n");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       printf("\n");       nhstepm is the number of hstepm from age to agelim 
       k++;       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 */
     while((c=getc(ficpar))=='#' && c!= EOF){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       ungetc(c,ficpar);       survival function given by stepm (the optimization length). Unfortunately it
       fgets(line, MAXLINE, ficpar);       means that if the survival funtion is printed only each two years of age and if
       puts(line);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fputs(line,ficparo);       results. So we changed our mind and took the option of the best precision.
     }    */
     ungetc(c,ficpar);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&ageminpar,&agemaxpar, &bage, &fage);    /* If stepm=6 months */
        /* nhstepm age range expressed in number of stepm */
     if (fage <= 2) {    agelim=AGESUP;
       bage = ageminpar;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
       fage = agemaxpar;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     }    /* if (stepm >= YEARM) hstepm=1;*/
        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     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\n",ageminpar,agemaxpar,bage,fage);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     while((c=getc(ficpar))=='#' && c!= EOF){    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     ungetc(c,ficpar);    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     fgets(line, MAXLINE, ficpar);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
     puts(line);  
     fputs(line,ficparo);    for (age=bage; age<=fage; age ++){ 
   }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   ungetc(c,ficpar);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        /* if (stepm >= YEARM) hstepm=1;*/
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      /* If stepm=6 months */
            /* Computed by stepm unit matrices, product of hstepma matrices, stored
   while((c=getc(ficpar))=='#' && c!= EOF){         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     ungetc(c,ficpar);      
     fgets(line, MAXLINE, ficpar);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     puts(line);  
     fputs(line,ficparo);      /* Computing  Variances of health expectancies */
   }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
   ungetc(c,ficpar);         decrease memory allocation */
        for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
   fscanf(ficpar,"pop_based=%d\n",&popbased);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
   fprintf(ficparo,"pop_based=%d\n",popbased);          hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
   fprintf(ficres,"pop_based=%d\n",popbased);      
          for(j=1; j<= nlstate; j++){
   while((c=getc(ficpar))=='#' && c!= EOF){          for(i=1; i<=nlstate; i++){
     ungetc(c,ficpar);            for(h=0; h<=nhstepm-1; h++){
     fgets(line, MAXLINE, ficpar);              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     puts(line);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
     fputs(line,ficparo);            }
   }          }
   ungetc(c,ficpar);        }
        
   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);        for(ij=1; ij<= nlstate*nlstate; ij++)
 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);          for(h=0; h<=nhstepm-1; h++){
 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);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
 while((c=getc(ficpar))=='#' && c!= EOF){      
     ungetc(c,ficpar);      
     fgets(line, MAXLINE, ficpar);      for(h=0; h<=nhstepm-1; h++)
     puts(line);        for(j=1; j<=nlstate*nlstate;j++)
     fputs(line,ficparo);          for(theta=1; theta <=npar; theta++)
   }            trgradg[h][j][theta]=gradg[h][theta][j];
   ungetc(c,ficpar);      
   
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);       for(ij=1;ij<=nlstate*nlstate;ij++)
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        for(ji=1;ji<=nlstate*nlstate;ji++)
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          varhe[ij][ji][(int)age] =0.;
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 /*------------ gnuplot -------------*/       for(h=0;h<=nhstepm-1;h++){
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);        for(k=0;k<=nhstepm-1;k++){
            matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
 /*------------ free_vector  -------------*/          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
  chdir(path);          for(ij=1;ij<=nlstate*nlstate;ij++)
              for(ji=1;ji<=nlstate*nlstate;ji++)
  free_ivector(wav,1,imx);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        }
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        }
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);      /* Computing expectancies */
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
  fclose(ficparo);      for(i=1; i<=nlstate;i++)
  fclose(ficres);        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 /*--------- index.htm --------*/            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast);            /* 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]);*/
   
            }
   /*--------------- Prevalence limit --------------*/  
        fprintf(ficresstdeij,"%3.0f",age );
   strcpy(filerespl,"pl");      for(i=1; i<=nlstate;i++){
   strcat(filerespl,fileres);        eip=0.;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        vip=0.;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        for(j=1; j<=nlstate;j++){
   }          eip += eij[i][j][(int)age];
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   fprintf(ficrespl,"#Prevalence limit\n");            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   fprintf(ficrespl,"#Age ");          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        }
   fprintf(ficrespl,"\n");        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
        }
   prlim=matrix(1,nlstate,1,nlstate);      fprintf(ficresstdeij,"\n");
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficrescveij,"%3.0f",age );
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(i=1; i<=nlstate;i++)
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1; j<=nlstate;j++){
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          cptj= (j-1)*nlstate+i;
   k=0;          for(i2=1; i2<=nlstate;i2++)
   agebase=ageminpar;            for(j2=1; j2<=nlstate;j2++){
   agelim=agemaxpar;              cptj2= (j2-1)*nlstate+i2;
   ftolpl=1.e-10;              if(cptj2 <= cptj)
   i1=cptcoveff;                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
   if (cptcovn < 1){i1=1;}            }
         }
   for(cptcov=1;cptcov<=i1;cptcov++){      fprintf(ficrescveij,"\n");
     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]);*/    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
         fprintf(ficrespl,"\n#******");    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
         for(j=1;j<=cptcoveff;j++)    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
         fprintf(ficrespl,"******\n");    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for (age=agebase; age<=agelim; age++){    printf("\n");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    fprintf(ficlog,"\n");
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)    free_vector(xm,1,npar);
           fprintf(ficrespl," %.5f", prlim[i][i]);    free_vector(xp,1,npar);
           fprintf(ficrespl,"\n");    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
         }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     }  }
   fclose(ficrespl);  
   /************ Variance ******************/
   /*------------- h Pij x at various ages ------------*/  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[])
    {
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    /* Variance of health expectancies */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    /* double **newm;*/
   }    double **dnewm,**doldm;
   printf("Computing pij: result on file '%s' \n", filerespij);    double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int k, cptcode;
   /*if (stepm<=24) stepsize=2;*/    double *xp;
     double **gp, **gm;  /* for var eij */
   agelim=AGESUP;    double ***gradg, ***trgradg; /*for var eij */
   hstepm=stepsize*YEARM; /* Every year of age */    double **gradgp, **trgradgp; /* for var p point j */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    double *gpp, *gmp; /* for var p point j */
      double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   k=0;    double ***p3mat;
   for(cptcov=1;cptcov<=i1;cptcov++){    double age,agelim, hf;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double ***mobaverage;
       k=k+1;    int theta;
         fprintf(ficrespij,"\n#****** ");    char digit[4];
         for(j=1;j<=cptcoveff;j++)    char digitp[25];
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");    char fileresprobmorprev[FILENAMELENGTH];
          
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    if(popbased==1){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      if(mobilav!=0)
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        strcpy(digitp,"-populbased-mobilav-");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      else strcpy(digitp,"-populbased-nomobil-");
           oldm=oldms;savm=savms;    }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      else 
           fprintf(ficrespij,"# Age");      strcpy(digitp,"-stablbased-");
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)    if (mobilav!=0) {
               fprintf(ficrespij," %1d-%1d",i,j);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           fprintf(ficrespij,"\n");      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           for (h=0; h<=nhstepm; h++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        printf(" Error in movingaverage mobilav=%d\n",mobilav);
             for(i=1; i<=nlstate;i++)      }
               for(j=1; j<=nlstate+ndeath;j++)    }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");    strcpy(fileresprobmorprev,"prmorprev"); 
           }    sprintf(digit,"%-d",ij);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
           fprintf(ficrespij,"\n");    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);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
   fclose(ficrespij);    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);
   /*---------- Forecasting ------------------*/    pstamp(ficresprobmorprev);
   if((stepm == 1) && (strcmp(model,".")==0)){    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);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     free_matrix(mint,1,maxwav,1,n);      fprintf(ficresprobmorprev," p.%-d SE",j);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      for(i=1; i<=nlstate;i++)
     free_vector(weight,1,n);}        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   else{    }  
     erreur=108;    fprintf(ficresprobmorprev,"\n");
     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(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);
   /*---------- Health expectancies and variances ------------*/  /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   strcpy(filerest,"t");    pstamp(ficresvij);
   strcat(filerest,fileres);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
   if((ficrest=fopen(filerest,"w"))==NULL) {    if(popbased==1)
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      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
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
   strcpy(filerese,"e");      for(j=1; j<=nlstate;j++)
   strcat(filerese,fileres);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    fprintf(ficresvij,"\n");
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }    xp=vector(1,npar);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
  strcpy(fileresv,"v");    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   strcat(fileresv,fileres);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   }    gpp=vector(nlstate+1,nlstate+ndeath);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   k=0;    
   for(cptcov=1;cptcov<=i1;cptcov++){    if(estepm < stepm){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      printf ("Problem %d lower than %d\n",estepm, stepm);
       k=k+1;    }
       fprintf(ficrest,"\n#****** ");    else  hstepm=estepm;   
       for(j=1;j<=cptcoveff;j++)    /* For example we decided to compute the life expectancy with the smallest unit */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       fprintf(ficrest,"******\n");       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
       fprintf(ficreseij,"\n#****** ");       Look at function hpijx to understand why (it is linked to memory size questions) */
       for(j=1;j<=cptcoveff;j++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       survival function given by stepm (the optimization length). Unfortunately it
       fprintf(ficreseij,"******\n");       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 
       fprintf(ficresvij,"\n#****** ");       results. So we changed our mind and took the option of the best precision.
       for(j=1;j<=cptcoveff;j++)    */
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       fprintf(ficresvij,"******\n");    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       oldm=oldms;savm=savms;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       oldm=oldms;savm=savms;      gp=matrix(0,nhstepm,1,nlstate);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      gm=matrix(0,nhstepm,1,nlstate);
      
   
        for(theta=1; theta <=npar; theta++){
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficrest,"\n");        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       epj=vector(1,nlstate+1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       for(age=bage; age <=fage ;age++){  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        if (popbased==1) {
         if (popbased==1) {          if(mobilav ==0){
           for(i=1; i<=nlstate;i++)            for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][k];              prlim[i][i]=probs[(int)age][i][ij];
         }          }else{ /* mobilav */ 
                    for(i=1; i<=nlstate;i++)
         fprintf(ficrest," %4.0f",age);              prlim[i][i]=mobaverage[(int)age][i][ij];
         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];    
           }        for(j=1; j<= nlstate; j++){
           epj[nlstate+1] +=epj[j];          for(h=0; h<=nhstepm; h++){
         }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
         for(i=1, vepp=0.;i <=nlstate;i++)              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           for(j=1;j <=nlstate;j++)          }
             vepp += vareij[i][j][(int)age];        }
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));        /* This for computing probability of death (h=1 means
         for(j=1;j <=nlstate;j++){           computed over hstepm matrices product = hstepm*stepm months) 
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));           as a weighted average of prlim.
         }        */
         fprintf(ficrest,"\n");        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 */
   fclose(ficreseij);  
   fclose(ficresvij);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   fclose(ficrest);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   fclose(ficpar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   free_vector(epj,1,nlstate+1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     
   /*------- Variance limit prevalence------*/          if (popbased==1) {
           if(mobilav ==0){
   strcpy(fileresvpl,"vpl");            for(i=1; i<=nlstate;i++)
   strcat(fileresvpl,fileres);              prlim[i][i]=probs[(int)age][i][ij];
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          }else{ /* mobilav */ 
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);            for(i=1; i<=nlstate;i++)
     exit(0);              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        }
   
   k=0;        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
   for(cptcov=1;cptcov<=i1;cptcov++){          for(h=0; h<=nhstepm; h++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       k=k+1;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       fprintf(ficresvpl,"\n#****** ");          }
       for(j=1;j<=cptcoveff;j++)        }
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        /* This for computing probability of death (h=1 means
       fprintf(ficresvpl,"******\n");           computed over hstepm matrices product = hstepm*stepm months) 
                 as a weighted average of prlim.
       varpl=matrix(1,nlstate,(int) bage, (int) fage);        */
       oldm=oldms;savm=savms;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
  }        }    
         /* end probability of death */
   fclose(ficresvpl);  
         for(j=1; j<= nlstate; j++) /* vareij */
   /*---------- End : free ----------------*/          for(h=0; h<=nhstepm; h++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
            gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
          }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      } /* End theta */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
    
   free_matrix(matcov,1,npar,1,npar);      for(h=0; h<=nhstepm; h++) /* veij */
   free_vector(delti,1,npar);        for(j=1; j<=nlstate;j++)
   free_matrix(agev,1,maxwav,1,imx);          for(theta=1; theta <=npar; theta++)
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);            trgradg[h][j][theta]=gradg[h][theta][j];
   
   if(erreur >0)      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     printf("End of Imach with error or warning %d\n",erreur);        for(theta=1; theta <=npar; theta++)
   else   printf("End of Imach\n");          trgradgp[j][theta]=gradgp[theta][j];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    
    
   /* 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);*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   /*printf("Total time was %d uSec.\n", total_usecs);*/      for(i=1;i<=nlstate;i++)
   /*------ End -----------*/        for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
  end:      for(h=0;h<=nhstepm;h++){
 #ifdef windows        for(k=0;k<=nhstepm;k++){
   /* chdir(pathcd);*/          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
 #endif          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
  /*system("wgnuplot graph.plt");*/          for(i=1;i<=nlstate;i++)
  /*system("../gp37mgw/wgnuplot graph.plt");*/            for(j=1;j<=nlstate;j++)
  /*system("cd ../gp37mgw");*/              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        }
  strcpy(plotcmd,GNUPLOTPROGRAM);      }
  strcat(plotcmd," ");    
  strcat(plotcmd,optionfilegnuplot);      /* pptj */
  system(plotcmd);      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);
 #ifdef windows      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   while (z[0] != 'q') {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     /* chdir(path); */          varppt[j][i]=doldmp[j][i];
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");      /* end ppptj */
     scanf("%s",z);      /*  x centered again */
     if (z[0] == 'c') system("./imach");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     else if (z[0] == 'e') system(optionfilehtm);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     else if (z[0] == 'g') system(plotcmd);   
     else if (z[0] == 'q') exit(0);      if (popbased==1) {
   }        if(mobilav ==0){
 #endif          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 **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     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,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     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,agelim, 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 from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">",nlstate, cpt, 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 m0,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 ******************/
   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, c, cptcod, i, h, i1;
     int *popage;
     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*************/
   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], cc[32];
     int i,j, k, l, 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 m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     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, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     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 */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       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 i1, 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);
   }
   
   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++;
           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\n",(int)moisdc[i],(int)andc[i],num[i],i);
           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\n",(int)moisdc[i],(int)andc[i],num[i],i);
           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;
                 }
               }
           }
           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);
   }
   
   
   /***********************************************/
   /**************** 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,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*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, fage, 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 kk1, kk2;
     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", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   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("Problem creating directory or it already exists %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);
   
     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");
   #elsedef
       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");
   #elsedef
       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 */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
             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.1.35  
changed lines
  Added in v.1.158


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