Diff for /imach/src/imach.c between versions 1.25 and 1.154

version 1.25, 2002/02/26 17:11:54 version 1.154, 2014/06/20 17:32:08
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.154  2014/06/20 17:32:08  brouard
      Summary: Outputs now all graphs of convergence to period prevalence
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.153  2014/06/20 16:45:46  brouard
   first survey ("cross") where individuals from different ages are    Summary: If 3 live state, convergence to period prevalence on same graph
   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    Revision 1.152  2014/06/18 17:54:09  brouard
   (if any) in individual health status.  Health expectancies are    Summary: open browser, use gnuplot on same dir than imach if not found in the path
   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    Revision 1.151  2014/06/18 16:43:30  brouard
   Maximum Likelihood of the parameters involved in the model.  The    *** empty log message ***
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.150  2014/06/18 16:42:35  brouard
   conditional to be observed in state i at the first wave. Therefore    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Author: brouard
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.149  2014/06/18 15:51:14  brouard
   where the markup *Covariates have to be included here again* invites    Summary: Some fixes in parameter files errors
   you to do it.  More covariates you add, slower the    Author: Nicolas Brouard
   convergence.  
     Revision 1.148  2014/06/17 17:38:48  brouard
   The advantage of this computer programme, compared to a simple    Summary: Nothing new
   multinomial logistic model, is clear when the delay between waves is not    Author: Brouard
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Just a new packaging for OS/X version 0.98nS
   account using an interpolation or extrapolation.    
     Revision 1.147  2014/06/16 10:33:11  brouard
   hPijx is the probability to be observed in state i at age x+h    *** empty log message ***
   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 1.146  2014/06/16 10:20:28  brouard
   states. This elementary transition (by month or quarter trimester,    Summary: Merge
   semester or year) is model as a multinomial logistic.  The hPx    Author: Brouard
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Merge, before building revised version.
   hPijx.  
     Revision 1.145  2014/06/10 21:23:15  brouard
   Also this programme outputs the covariance matrix of the parameters but also    Summary: Debugging with valgrind
   of the life expectancies. It also computes the prevalence limits.    Author: Nicolas Brouard
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Lot of changes in order to output the results with some covariates
            Institut national d'études démographiques, Paris.    After the Edimburgh REVES conference 2014, it seems mandatory to
   This software have been partly granted by Euro-REVES, a concerted action    improve the code.
   from the European Union.    No more memory valgrind error but a lot has to be done in order to
   It is copyrighted identically to a GNU software product, ie programme and    continue the work of splitting the code into subroutines.
   software can be distributed freely for non commercial use. Latest version    Also, decodemodel has been improved. Tricode is still not
   can be accessed at http://euroreves.ined.fr/imach .    optimal. nbcode should be improved. Documentation has been added in
   **********************************************************************/    the source code.
    
 #include <math.h>    Revision 1.143  2014/01/26 09:45:38  brouard
 #include <stdio.h>    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 #include <stdlib.h>  
 #include <unistd.h>    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
     (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 #define MAXLINE 256  
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Revision 1.142  2014/01/26 03:57:36  brouard
 #define FILENAMELENGTH 80    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 /*#define DEBUG*/  
 #define windows    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.141  2014/01/26 02:42:01  brouard
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.140  2011/09/02 10:37:54  brouard
     Summary: times.h is ok with mingw32 now.
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.139  2010/06/14 07:50:17  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 #define NCOVMAX 8 /* Maximum number of covariates */    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.138  2010/04/30 18:19:40  brouard
 #define AGESUP 130    *** empty log message ***
 #define AGEBASE 40  
     Revision 1.137  2010/04/29 18:11:38  brouard
     (Module): Checking covariates for more complex models
 int erreur; /* Error number */    than V1+V2. A lot of change to be done. Unstable.
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.136  2010/04/26 20:30:53  brouard
 int npar=NPARMAX;    (Module): merging some libgsl code. Fixing computation
 int nlstate=2; /* Number of live states */    of likelione (using inter/intrapolation if mle = 0) in order to
 int ndeath=1; /* Number of dead states */    get same likelihood as if mle=1.
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Some cleaning of code and comments added.
 int popbased=0;  
     Revision 1.135  2009/10/29 15:33:14  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.134  2009/10/29 13:18:53  brouard
 int mle, weightopt;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 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 1.133  2009/07/06 10:21:25  brouard
 double jmean; /* Mean space between 2 waves */    just nforces
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.132  2009/07/06 08:22:05  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    Many tings
 FILE *ficgp,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.131  2009/06/20 16:22:47  brouard
   char filerese[FILENAMELENGTH];    Some dimensions resccaled
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.130  2009/05/26 06:44:34  brouard
  FILE  *ficresvpl;    (Module): Max Covariate is now set to 20 instead of 8. A
   char fileresvpl[FILENAMELENGTH];    lot of cleaning with variables initialized to 0. Trying to make
     V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.129  2007/08/31 13:49:27  lievre
 #define FTOL 1.0e-10    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 NRANSI    Revision 1.128  2006/06/30 13:02:05  brouard
 #define ITMAX 200    (Module): Clarifications on computing e.j
   
 #define TOL 2.0e-4    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 #define CGOLD 0.3819660    imach-114 because nhstepm was no more computed in the age
 #define ZEPS 1.0e-10    loop. Now we define nhstepma in the age loop.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
 #define GOLD 1.618034    and then all the health expectancies with variances or standard
 #define GLIMIT 100.0    deviation (needs data from the Hessian matrices) which slows the
 #define TINY 1.0e-20    computation.
     In the future we should be able to stop the program is only health
 static double maxarg1,maxarg2;    expectancies and graph are needed without standard deviations.
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.126  2006/04/28 17:23:28  brouard
      (Module): Yes the sum of survivors was wrong since
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    imach-114 because nhstepm was no more computed in the age
 #define rint(a) floor(a+0.5)    loop. Now we define nhstepma in the age loop.
     Version 0.98h
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.125  2006/04/04 15:20:31  lievre
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Errors in calculation of health expectancies. Age was not initialized.
     Forecasting file added.
 int imx;  
 int stepm;    Revision 1.124  2006/03/22 17:13:53  lievre
 /* Stepm, step in month: minimum step interpolation*/    Parameters are printed with %lf instead of %f (more numbers after the comma).
     The log-likelihood is printed in the log file
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.123  2006/03/20 10:52:43  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    * imach.c (Module): <title> changed, corresponds to .htm file
 double **pmmij, ***probs, ***mobaverage;    name. <head> headers where missing.
 double dateintmean=0;  
     * imach.c (Module): Weights can have a decimal point as for
 double *weight;    English (a comma might work with a correct LC_NUMERIC environment,
 int **s; /* Status */    otherwise the weight is truncated).
 double *agedc, **covar, idx;    Modification of warning when the covariates values are not 0 or
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    1.
     Version 0.98g
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
 /**************** split *************************/    English (a comma might work with a correct LC_NUMERIC environment,
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    otherwise the weight is truncated).
 {    Modification of warning when the covariates values are not 0 or
    char *s;                             /* pointer */    1.
    int  l1, l2;                         /* length counters */    Version 0.98g
   
    l1 = strlen( path );                 /* length of path */    Revision 1.121  2006/03/16 17:45:01  lievre
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    * imach.c (Module): Comments concerning covariates added
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */    * imach.c (Module): refinements in the computation of lli if
 #else    status=-2 in order to have more reliable computation if stepm is
    s = strrchr( path, '/' );            /* find last / */    not 1 month. Version 0.98f
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.120  2006/03/16 15:10:38  lievre
 #if     defined(__bsd__)                /* get current working directory */    (Module): refinements in the computation of lli if
       extern char       *getwd( );    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
       if ( getwd( dirc ) == NULL ) {  
 #else    Revision 1.119  2006/03/15 17:42:26  brouard
       extern char       *getcwd( );    (Module): Bug if status = -2, the loglikelihood was
     computed as likelihood omitting the logarithm. Version O.98e
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.118  2006/03/14 18:20:07  brouard
          return( GLOCK_ERROR_GETCWD );    (Module): varevsij Comments added explaining the second
       }    table of variances if popbased=1 .
       strcpy( name, path );             /* we've got it */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    } else {                             /* strip direcotry from path */    (Module): Function pstamp added
       s++;                              /* after this, the filename */    (Module): Version 0.98d
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.117  2006/03/14 17:16:22  brouard
       strcpy( name, s );                /* save file name */    (Module): varevsij Comments added explaining the second
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    table of variances if popbased=1 .
       dirc[l1-l2] = 0;                  /* add zero */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    }    (Module): Function pstamp added
    l1 = strlen( dirc );                 /* length of directory */    (Module): Version 0.98d
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.116  2006/03/06 10:29:27  brouard
 #else    (Module): Variance-covariance wrong links and
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    varian-covariance of ej. is needed (Saito).
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.115  2006/02/27 12:17:45  brouard
    s++;    (Module): One freematrix added in mlikeli! 0.98c
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Revision 1.114  2006/02/26 12:57:58  brouard
    l2= strlen( s)+1;    (Module): Some improvements in processing parameter
    strncpy( finame, name, l1-l2);    filename with strsep.
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    Revision 1.113  2006/02/24 14:20:24  brouard
 }    (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
 /******************************************/  
     Revision 1.112  2006/01/30 09:55:26  brouard
 void replace(char *s, char*t)    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 {  
   int i;    Revision 1.111  2006/01/25 20:38:18  brouard
   int lg=20;    (Module): Lots of cleaning and bugs added (Gompertz)
   i=0;    (Module): Comments can be added in data file. Missing date values
   lg=strlen(t);    can be a simple dot '.'.
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.110  2006/01/25 00:51:50  brouard
     if (t[i]== '\\') s[i]='/';    (Module): Lots of cleaning and bugs added (Gompertz)
   }  
 }    Revision 1.109  2006/01/24 19:37:15  brouard
     (Module): Comments (lines starting with a #) are allowed in data.
 int nbocc(char *s, char occ)  
 {    Revision 1.108  2006/01/19 18:05:42  lievre
   int i,j=0;    Gnuplot problem appeared...
   int lg=20;    To be fixed
   i=0;  
   lg=strlen(s);    Revision 1.107  2006/01/19 16:20:37  brouard
   for(i=0; i<= lg; i++) {    Test existence of gnuplot in imach path
   if  (s[i] == occ ) j++;  
   }    Revision 1.106  2006/01/19 13:24:36  brouard
   return j;    Some cleaning and links added in html output
 }  
     Revision 1.105  2006/01/05 20:23:19  lievre
 void cutv(char *u,char *v, char*t, char occ)    *** empty log message ***
 {  
   int i,lg,j,p=0;    Revision 1.104  2005/09/30 16:11:43  lievre
   i=0;    (Module): sump fixed, loop imx fixed, and simplifications.
   for(j=0; j<=strlen(t)-1; j++) {    (Module): If the status is missing at the last wave but we know
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    that the person is alive, then we can code his/her status as -2
   }    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
   lg=strlen(t);    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   for(j=0; j<p; j++) {    the healthy state at last known wave). Version is 0.98
     (u[j] = t[j]);  
   }    Revision 1.103  2005/09/30 15:54:49  lievre
      u[p]='\0';    (Module): sump fixed, loop imx fixed, and simplifications.
   
    for(j=0; j<= lg; j++) {    Revision 1.102  2004/09/15 17:31:30  brouard
     if (j>=(p+1))(v[j-p-1] = t[j]);    Add the possibility to read data file including tab characters.
   }  
 }    Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
 /********************** nrerror ********************/  
     Revision 1.100  2004/07/12 18:29:06  brouard
 void nrerror(char error_text[])    Add version for Mac OS X. Just define UNIX in Makefile
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.99  2004/06/05 08:57:40  brouard
   fprintf(stderr,"%s\n",error_text);    *** empty log message ***
   exit(1);  
 }    Revision 1.98  2004/05/16 15:05:56  brouard
 /*********************** vector *******************/    New version 0.97 . First attempt to estimate force of mortality
 double *vector(int nl, int nh)    directly from the data i.e. without the need of knowing the health
 {    state at each age, but using a Gompertz model: log u =a + b*age .
   double *v;    This is the basic analysis of mortality and should be done before any
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    other analysis, in order to test if the mortality estimated from the
   if (!v) nrerror("allocation failure in vector");    cross-longitudinal survey is different from the mortality estimated
   return v-nl+NR_END;    from other sources like vital statistic data.
 }  
     The same imach parameter file can be used but the option for mle should be -3.
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Agnès, who wrote this part of the code, tried to keep most of the
 {    former routines in order to include the new code within the former code.
   free((FREE_ARG)(v+nl-NR_END));  
 }    The output is very simple: only an estimate of the intercept and of
     the slope with 95% confident intervals.
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Current limitations:
 {    A) Even if you enter covariates, i.e. with the
   int *v;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    B) There is no computation of Life Expectancy nor Life Table.
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;    Revision 1.97  2004/02/20 13:25:42  lievre
 }    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    Revision 1.96  2003/07/15 15:38:55  brouard
 {    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   free((FREE_ARG)(v+nl-NR_END));    rewritten within the same printf. Workaround: many printfs.
 }  
     Revision 1.95  2003/07/08 07:54:34  brouard
 /******************* imatrix *******************************/    * imach.c (Repository):
 int **imatrix(long nrl, long nrh, long ncl, long nch)    (Repository): Using imachwizard code to output a more meaningful covariance
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    matrix (cov(a12,c31) instead of numbers.
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Revision 1.94  2003/06/27 13:00:02  brouard
   int **m;    Just cleaning
    
   /* allocate pointers to rows */    Revision 1.93  2003/06/25 16:33:55  brouard
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    (Module): On windows (cygwin) function asctime_r doesn't
   if (!m) nrerror("allocation failure 1 in matrix()");    exist so I changed back to asctime which exists.
   m += NR_END;    (Module): Version 0.96b
   m -= nrl;  
      Revision 1.92  2003/06/25 16:30:45  brouard
      (Module): On windows (cygwin) function asctime_r doesn't
   /* allocate rows and set pointers to them */    exist so I changed back to asctime which exists.
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.91  2003/06/25 15:30:29  brouard
   m[nrl] += NR_END;    * imach.c (Repository): Duplicated warning errors corrected.
   m[nrl] -= ncl;    (Repository): Elapsed time after each iteration is now output. It
      helps to forecast when convergence will be reached. Elapsed time
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    is stamped in powell.  We created a new html file for the graphs
      concerning matrix of covariance. It has extension -cov.htm.
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.90  2003/06/24 12:34:15  brouard
 }    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 /****************** free_imatrix *************************/    of the covariance matrix to be input.
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    Revision 1.89  2003/06/24 12:30:52  brouard
       long nch,ncl,nrh,nrl;    (Module): Some bugs corrected for windows. Also, when
      /* free an int matrix allocated by imatrix() */    mle=-1 a template is output in file "or"mypar.txt with the design
 {    of the covariance matrix to be input.
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Revision 1.88  2003/06/23 17:54:56  brouard
 }    * 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.
   
 /******************* matrix *******************************/    Revision 1.87  2003/06/18 12:26:01  brouard
 double **matrix(long nrl, long nrh, long ncl, long nch)    Version 0.96
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    Revision 1.86  2003/06/17 20:04:08  brouard
   double **m;    (Module): Change position of html and gnuplot routines and added
     routine fileappend.
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.85  2003/06/17 13:12:43  brouard
   m += NR_END;    * imach.c (Repository): Check when date of death was earlier that
   m -= nrl;    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    was wrong (infinity). We still send an "Error" but patch by
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    assuming that the date of death was just one stepm after the
   m[nrl] += NR_END;    interview.
   m[nrl] -= ncl;    (Repository): Because some people have very long ID (first column)
     we changed int to long in num[] and we added a new lvector for
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    memory allocation. But we also truncated to 8 characters (left
   return m;    truncation)
 }    (Repository): No more line truncation errors.
   
 /*************************free matrix ************************/    Revision 1.84  2003/06/13 21:44:43  brouard
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    * imach.c (Repository): Replace "freqsummary" at a correct
 {    place. It differs from routine "prevalence" which may be called
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    many times. Probs is memory consuming and must be used with
   free((FREE_ARG)(m+nrl-NR_END));    parcimony.
 }    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 /******************* ma3x *******************************/    Revision 1.83  2003/06/10 13:39:11  lievre
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    *** empty log message ***
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Revision 1.82  2003/06/05 15:57:20  brouard
   double ***m;    Add log in  imach.c and  fullversion number is now printed.
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  */
   if (!m) nrerror("allocation failure 1 in matrix()");  /*
   m += NR_END;     Interpolated Markov Chain
   m -= nrl;  
     Short summary of the programme:
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    This program computes Healthy Life Expectancies from
   m[nrl] += NR_END;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   m[nrl] -= ncl;    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    (if any) in individual health status.  Health expectancies are
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    computed from the time spent in each health state according to a
   m[nrl][ncl] += NR_END;    model. More health states you consider, more time is necessary to reach the
   m[nrl][ncl] -= nll;    Maximum Likelihood of the parameters involved in the model.  The
   for (j=ncl+1; j<=nch; j++)    simplest model is the multinomial logistic model where pij is the
     m[nrl][j]=m[nrl][j-1]+nlay;    probability to be observed in state j at the second wave
      conditional to be observed in state i at the first wave. Therefore
   for (i=nrl+1; i<=nrh; i++) {    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    'age' is age and 'sex' is a covariate. If you want to have a more
     for (j=ncl+1; j<=nch; j++)    complex model than "constant and age", you should modify the program
       m[i][j]=m[i][j-1]+nlay;    where the markup *Covariates have to be included here again* invites
   }    you to do it.  More covariates you add, slower the
   return m;    convergence.
 }  
     The advantage of this computer programme, compared to a simple
 /*************************free ma3x ************************/    multinomial logistic model, is clear when the delay between waves is not
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    identical for each individual. Also, if a individual missed an
 {    intermediate interview, the information is lost, but taken into
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    account using an interpolation or extrapolation.  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    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
     split into an exact number (nh*stepm) of unobserved intermediate
 /***************** f1dim *************************/    states. This elementary transition (by month, quarter,
 extern int ncom;    semester or year) is modelled as a multinomial logistic.  The hPx
 extern double *pcom,*xicom;    matrix is simply the matrix product of nh*stepm elementary matrices
 extern double (*nrfunc)(double []);    and the contribution of each individual to the likelihood is simply
      hPijx.
 double f1dim(double x)  
 {    Also this programme outputs the covariance matrix of the parameters but also
   int j;    of the life expectancies. It also computes the period (stable) prevalence. 
   double f;    
   double *xt;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
               Institut national d'études démographiques, Paris.
   xt=vector(1,ncom);    This software have been partly granted by Euro-REVES, a concerted action
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    from the European Union.
   f=(*nrfunc)(xt);    It is copyrighted identically to a GNU software product, ie programme and
   free_vector(xt,1,ncom);    software can be distributed freely for non commercial use. Latest version
   return f;    can be accessed at http://euroreves.ined.fr/imach .
 }  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 /*****************brent *************************/    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    
 {    **********************************************************************/
   int iter;  /*
   double a,b,d,etemp;    main
   double fu,fv,fw,fx;    read parameterfile
   double ftemp;    read datafile
   double p,q,r,tol1,tol2,u,v,w,x,xm;    concatwav
   double e=0.0;    freqsummary
      if (mle >= 1)
   a=(ax < cx ? ax : cx);      mlikeli
   b=(ax > cx ? ax : cx);    print results files
   x=w=v=bx;    if mle==1 
   fw=fv=fx=(*f)(x);       computes hessian
   for (iter=1;iter<=ITMAX;iter++) {    read end of parameter file: agemin, agemax, bage, fage, estepm
     xm=0.5*(a+b);        begin-prev-date,...
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    open gnuplot file
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    open html file
     printf(".");fflush(stdout);    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
 #ifdef DEBUG     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
     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);                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */      freexexit2 possible for memory heap.
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    h Pij x                         | pij_nom  ficrestpij
       *xmin=x;     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
       return fx;         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
     }         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
     ftemp=fu;  
     if (fabs(e) > tol1) {         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
       r=(x-w)*(fx-fv);         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
       q=(x-v)*(fx-fw);    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
       p=(x-v)*q-(x-w)*r;     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
       q=2.0*(q-r);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
       if (q > 0.0) p = -p;  
       q=fabs(q);    forecasting if prevfcast==1 prevforecast call prevalence()
       etemp=e;    health expectancies
       e=d;    Variance-covariance of DFLE
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    prevalence()
         d=CGOLD*(e=(x >= xm ? a-x : b-x));     movingaverage()
       else {    varevsij() 
         d=p/q;    if popbased==1 varevsij(,popbased)
         u=x+d;    total life expectancies
         if (u-a < tol2 || b-u < tol2)    Variance of period (stable) prevalence
           d=SIGN(tol1,xm-x);   end
       }  */
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));   
     fu=(*f)(u);  #include <math.h>
     if (fu <= fx) {  #include <stdio.h>
       if (u >= x) a=x; else b=x;  #include <stdlib.h>
       SHFT(v,w,x,u)  #include <string.h>
         SHFT(fv,fw,fx,fu)  #include <unistd.h>
         } else {  
           if (u < x) a=u; else b=u;  #include <limits.h>
           if (fu <= fw || w == x) {  #include <sys/types.h>
             v=w;  #include <sys/stat.h>
             w=u;  #include <errno.h>
             fv=fw;  extern int errno;
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  #ifdef LINUX
             v=u;  #include <time.h>
             fv=fu;  #include "timeval.h"
           }  #else
         }  #include <sys/time.h>
   }  #endif
   nrerror("Too many iterations in brent");  
   *xmin=x;  #ifdef GSL
   return fx;  #include <gsl/gsl_errno.h>
 }  #include <gsl/gsl_multimin.h>
   #endif
 /****************** mnbrak ***********************/  
   /* #include <libintl.h> */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  /* #define _(String) gettext (String) */
             double (*func)(double))  
 {  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   double ulim,u,r,q, dum;  
   double fu;  #define GNUPLOTPROGRAM "gnuplot"
    /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   *fa=(*func)(*ax);  #define FILENAMELENGTH 132
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
     SHFT(dum,*ax,*bx,dum)  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       SHFT(dum,*fb,*fa,dum)  
       }  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
   *cx=(*bx)+GOLD*(*bx-*ax);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  #define NINTERVMAX 8
     r=(*bx-*ax)*(*fb-*fc);  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
     q=(*bx-*cx)*(*fb-*fa);  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define MAXN 20000
     if ((*bx-u)*(u-*cx) > 0.0) {  #define YEARM 12. /**< Number of months per year */
       fu=(*func)(u);  #define AGESUP 130
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define AGEBASE 40
       fu=(*func)(u);  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
       if (fu < *fc) {  #ifdef UNIX
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define DIRSEPARATOR '/'
           SHFT(*fb,*fc,fu,(*func)(u))  #define CHARSEPARATOR "/"
           }  #define ODIRSEPARATOR '\\'
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  #else
       u=ulim;  #define DIRSEPARATOR '\\'
       fu=(*func)(u);  #define CHARSEPARATOR "\\"
     } else {  #define ODIRSEPARATOR '/'
       u=(*cx)+GOLD*(*cx-*bx);  #endif
       fu=(*func)(u);  
     }  /* $Id$ */
     SHFT(*ax,*bx,*cx,u)  /* $State$ */
       SHFT(*fa,*fb,*fc,fu)  
       }  char version[]="Imach version 0.98nU, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
 }  char fullversion[]="$Revision$ $Date$"; 
   char strstart[80];
 /*************** linmin ************************/  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int ncom;  int nvar=0, nforce=0; /* Number of variables, number of forces */
 double *pcom,*xicom;  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
 double (*nrfunc)(double []);  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
    int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
 {  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   double brent(double ax, double bx, double cx,  int cptcovprodnoage=0; /**< Number of covariate products without age */   
                double (*f)(double), double tol, double *xmin);  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   double f1dim(double x);  int cptcov=0; /* Working variable */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  int npar=NPARMAX;
               double *fc, double (*func)(double));  int nlstate=2; /* Number of live states */
   int j;  int ndeath=1; /* Number of dead states */
   double xx,xmin,bx,ax;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   double fx,fb,fa;  int popbased=0;
    
   ncom=n;  int *wav; /* Number of waves for this individuual 0 is possible */
   pcom=vector(1,n);  int maxwav=0; /* Maxim number of waves */
   xicom=vector(1,n);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   nrfunc=func;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   for (j=1;j<=n;j++) {  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     pcom[j]=p[j];                     to the likelihood and the sum of weights (done by funcone)*/
     xicom[j]=xi[j];  int mle=1, weightopt=0;
   }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   ax=0.0;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   xx=1.0;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  double jmean=1; /* Mean space between 2 waves */
 #ifdef DEBUG  double **matprod2(); /* test */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double **oldm, **newm, **savm; /* Working pointers to matrices */
 #endif  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   for (j=1;j<=n;j++) {  /*FILE *fic ; */ /* Used in readdata only */
     xi[j] *= xmin;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     p[j] += xi[j];  FILE *ficlog, *ficrespow;
   }  int globpr=0; /* Global variable for printing or not */
   free_vector(xicom,1,n);  double fretone; /* Only one call to likelihood */
   free_vector(pcom,1,n);  long ipmx=0; /* Number of contributions */
 }  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
 /*************** powell ************************/  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  FILE *ficresilk;
             double (*func)(double []))  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 {  FILE *ficresprobmorprev;
   void linmin(double p[], double xi[], int n, double *fret,  FILE *fichtm, *fichtmcov; /* Html File */
               double (*func)(double []));  FILE *ficreseij;
   int i,ibig,j;  char filerese[FILENAMELENGTH];
   double del,t,*pt,*ptt,*xit;  FILE *ficresstdeij;
   double fp,fptt;  char fileresstde[FILENAMELENGTH];
   double *xits;  FILE *ficrescveij;
   pt=vector(1,n);  char filerescve[FILENAMELENGTH];
   ptt=vector(1,n);  FILE  *ficresvij;
   xit=vector(1,n);  char fileresv[FILENAMELENGTH];
   xits=vector(1,n);  FILE  *ficresvpl;
   *fret=(*func)(p);  char fileresvpl[FILENAMELENGTH];
   for (j=1;j<=n;j++) pt[j]=p[j];  char title[MAXLINE];
   for (*iter=1;;++(*iter)) {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     fp=(*fret);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     ibig=0;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     del=0.0;  char command[FILENAMELENGTH];
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  int  outcmd=0;
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     printf("\n");  
     for (i=1;i<=n;i++) {  char filelog[FILENAMELENGTH]; /* Log file */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  char filerest[FILENAMELENGTH];
       fptt=(*fret);  char fileregp[FILENAMELENGTH];
 #ifdef DEBUG  char popfile[FILENAMELENGTH];
       printf("fret=%lf \n",*fret);  
 #endif  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
       if (fabs(fptt-(*fret)) > del) {  struct timezone tzp;
         del=fabs(fptt-(*fret));  extern int gettimeofday();
         ibig=i;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
       }  long time_value;
 #ifdef DEBUG  extern long time();
       printf("%d %.12e",i,(*fret));  char strcurr[80], strfor[80];
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  char *endptr;
         printf(" x(%d)=%.12e",j,xit[j]);  long lval;
       }  double dval;
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);  #define NR_END 1
       printf("\n");  #define FREE_ARG char*
 #endif  #define FTOL 1.0e-10
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #define NRANSI 
 #ifdef DEBUG  #define ITMAX 200 
       int k[2],l;  
       k[0]=1;  #define TOL 2.0e-4 
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  #define CGOLD 0.3819660 
       for (j=1;j<=n;j++)  #define ZEPS 1.0e-10 
         printf(" %.12e",p[j]);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       printf("\n");  
       for(l=0;l<=1;l++) {  #define GOLD 1.618034 
         for (j=1;j<=n;j++) {  #define GLIMIT 100.0 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  #define TINY 1.0e-20 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }  static double maxarg1,maxarg2;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       }  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 #endif    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  static double sqrarg;
       free_vector(ptt,1,n);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       free_vector(pt,1,n);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       return;  int agegomp= AGEGOMP;
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  int imx; 
     for (j=1;j<=n;j++) {  int stepm=1;
       ptt[j]=2.0*p[j]-pt[j];  /* Stepm, step in month: minimum step interpolation*/
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  int estepm;
     }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     fptt=(*func)(ptt);  
     if (fptt < fp) {  int m,nb;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  long *num;
       if (t < 0.0) {  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
         linmin(p,xit,n,fret,func);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
         for (j=1;j<=n;j++) {  double **pmmij, ***probs;
           xi[j][ibig]=xi[j][n];  double *ageexmed,*agecens;
           xi[j][n]=xit[j];  double dateintmean=0;
         }  
 #ifdef DEBUG  double *weight;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int **s; /* Status */
         for(j=1;j<=n;j++)  double *agedc;
           printf(" %.12e",xit[j]);  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
         printf("\n");                    * covar=matrix(0,NCOVMAX,1,n); 
 #endif                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       }  double  idx; 
     }  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   }  int *Ndum; /** Freq of modality (tricode */
 }  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   int **Tvard, *Tprod, cptcovprod, *Tvaraff;
 /**** Prevalence limit ****************/  double *lsurv, *lpop, *tpop;
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
 {  double ftolhess; /**< Tolerance for computing hessian */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   int i, ii,j,k;  {
   double min, max, maxmin, maxmax,sumnew=0.;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   double **matprod2();       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   double **out, cov[NCOVMAX], **pmij();    */ 
   double **newm;    char  *ss;                            /* pointer */
   double agefin, delaymax=50 ; /* Max number of years to converge */    int   l1, l2;                         /* length counters */
   
   for (ii=1;ii<=nlstate+ndeath;ii++)    l1 = strlen(path );                   /* length of path */
     for (j=1;j<=nlstate+ndeath;j++){    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     }    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       strcpy( name, path );               /* we got the fullname name because no directory */
    cov[1]=1.;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
          printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      /* get current working directory */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      /*    extern  char* getcwd ( char *buf , int len);*/
     newm=savm;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     /* Covariates have to be included here again */        return( GLOCK_ERROR_GETCWD );
      cov[2]=agefin;      }
        /* got dirc from getcwd*/
       for (k=1; k<=cptcovn;k++) {      printf(" DIRC = %s \n",dirc);
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    } else {                              /* strip direcotry from path */
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/      ss++;                               /* after this, the filename */
       }      l2 = strlen( ss );                  /* length of filename */
       for (k=1; k<=cptcovage;k++)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      strcpy( name, ss );         /* save file name */
       for (k=1; k<=cptcovprod;k++)      strncpy( dirc, path, l1 - l2 );     /* now the directory */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      dirc[l1-l2] = 0;                    /* add zero */
       printf(" DIRC2 = %s \n",dirc);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    }
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    /* We add a separator at the end of dirc if not exists */
     l1 = strlen( dirc );                  /* length of directory */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    if( dirc[l1-1] != DIRSEPARATOR ){
       dirc[l1] =  DIRSEPARATOR;
     savm=oldm;      dirc[l1+1] = 0; 
     oldm=newm;      printf(" DIRC3 = %s \n",dirc);
     maxmax=0.;    }
     for(j=1;j<=nlstate;j++){    ss = strrchr( name, '.' );            /* find last / */
       min=1.;    if (ss >0){
       max=0.;      ss++;
       for(i=1; i<=nlstate; i++) {      strcpy(ext,ss);                     /* save extension */
         sumnew=0;      l1= strlen( name);
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      l2= strlen(ss)+1;
         prlim[i][j]= newm[i][j]/(1-sumnew);      strncpy( finame, name, l1-l2);
         max=FMAX(max,prlim[i][j]);      finame[l1-l2]= 0;
         min=FMIN(min,prlim[i][j]);    }
       }  
       maxmin=max-min;    return( 0 );                          /* we're done */
       maxmax=FMAX(maxmax,maxmin);  }
     }  
     if(maxmax < ftolpl){  
       return prlim;  /******************************************/
     }  
   }  void replace_back_to_slash(char *s, char*t)
 }  {
     int i;
 /*************** transition probabilities ***************/    int lg=0;
     i=0;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    lg=strlen(t);
 {    for(i=0; i<= lg; i++) {
   double s1, s2;      (s[i] = t[i]);
   /*double t34;*/      if (t[i]== '\\') s[i]='/';
   int i,j,j1, nc, ii, jj;    }
   }
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){  char *trimbb(char *out, char *in)
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
         /*s2 += param[i][j][nc]*cov[nc];*/    char *s;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    s=out;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    while (*in != '\0'){
       }      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
       ps[i][j]=s2;        in++;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      }
     }      *out++ = *in++;
     for(j=i+1; j<=nlstate+ndeath;j++){    }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    *out='\0';
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    return s;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  }
       }  
       ps[i][j]=s2;  char *cutl(char *blocc, char *alocc, char *in, char occ)
     }  {
   }    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
     /*ps[3][2]=1;*/       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef2ghi" and alocc="j".
   for(i=1; i<= nlstate; i++){       If occ is not found blocc is null and alocc is equal to in. Returns blocc
      s1=0;    */
     for(j=1; j<i; j++)    char *s, *t, *bl;
       s1+=exp(ps[i][j]);    t=in;s=in;
     for(j=i+1; j<=nlstate+ndeath; j++)    while ((*in != occ) && (*in != '\0')){
       s1+=exp(ps[i][j]);      *alocc++ = *in++;
     ps[i][i]=1./(s1+1.);    }
     for(j=1; j<i; j++)    if( *in == occ){
       ps[i][j]= exp(ps[i][j])*ps[i][i];      *(alocc)='\0';
     for(j=i+1; j<=nlstate+ndeath; j++)      s=++in;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    }
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */   
   } /* end i */    if (s == t) {/* occ not found */
       *(alocc-(in-s))='\0';
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      in=s;
     for(jj=1; jj<= nlstate+ndeath; jj++){    }
       ps[ii][jj]=0;    while ( *in != '\0'){
       ps[ii][ii]=1;      *blocc++ = *in++;
     }    }
   }  
     *blocc='\0';
     return t;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  char *cutv(char *blocc, char *alocc, char *in, char occ)
      printf("%lf ",ps[ii][jj]);  {
    }    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
     printf("\n ");       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     }       gives blocc="abcdef2ghi" and alocc="j".
     printf("\n ");printf("%lf ",cov[2]);*/       If occ is not found blocc is null and alocc is equal to in. Returns alocc
 /*    */
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    char *s, *t;
   goto end;*/    t=in;s=in;
     return ps;    while (*in != '\0'){
 }      while( *in == occ){
         *blocc++ = *in++;
 /**************** Product of 2 matrices ******************/        s=in;
       }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      *blocc++ = *in++;
 {    }
   /* 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(...) */      *(blocc-(in-s))='\0';
   /* in, b, out are matrice of pointers which should have been initialized    else
      before: only the contents of out is modified. The function returns      *(blocc-(in-s)-1)='\0';
      a pointer to pointers identical to out */    in=s;
   long i, j, k;    while ( *in != '\0'){
   for(i=nrl; i<= nrh; i++)      *alocc++ = *in++;
     for(k=ncolol; k<=ncoloh; k++)    }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];    *alocc='\0';
     return s;
   return out;  }
 }  
   int nbocc(char *s, char occ)
   {
 /************* Higher Matrix Product ***************/    int i,j=0;
     int lg=20;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    i=0;
 {    lg=strlen(s);
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    for(i=0; i<= lg; i++) {
      duration (i.e. until    if  (s[i] == occ ) j++;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    }
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    return j;
      (typically every 2 years instead of every month which is too big).  }
      Model is determined by parameters x and covariates have to be  
      included manually here.  /* void cutv(char *u,char *v, char*t, char occ) */
   /* { */
      */  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   int i, j, d, h, k;  /*      gives u="abcdef2ghi" and v="j" *\/ */
   double **out, cov[NCOVMAX];  /*   int i,lg,j,p=0; */
   double **newm;  /*   i=0; */
   /*   lg=strlen(t); */
   /* Hstepm could be zero and should return the unit matrix */  /*   for(j=0; j<=lg-1; j++) { */
   for (i=1;i<=nlstate+ndeath;i++)  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
     for (j=1;j<=nlstate+ndeath;j++){  /*   } */
       oldm[i][j]=(i==j ? 1.0 : 0.0);  
       po[i][j][0]=(i==j ? 1.0 : 0.0);  /*   for(j=0; j<p; j++) { */
     }  /*     (u[j] = t[j]); */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /*   } */
   for(h=1; h <=nhstepm; h++){  /*      u[p]='\0'; */
     for(d=1; d <=hstepm; d++){  
       newm=savm;  /*    for(j=0; j<= lg; j++) { */
       /* Covariates have to be included here again */  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
       cov[1]=1.;  /*   } */
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /* } */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
       for (k=1; k<=cptcovage;k++)  /********************** nrerror ********************/
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  void nrerror(char error_text[])
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  {
     fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    exit(EXIT_FAILURE);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  }
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  /*********************** vector *******************/
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  double *vector(int nl, int nh)
       savm=oldm;  {
       oldm=newm;    double *v;
     }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     for(i=1; i<=nlstate+ndeath; i++)    if (!v) nrerror("allocation failure in vector");
       for(j=1;j<=nlstate+ndeath;j++) {    return v-nl+NR_END;
         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]);  
          */  /************************ free vector ******************/
       }  void free_vector(double*v, int nl, int nh)
   } /* end h */  {
   return po;    free((FREE_ARG)(v+nl-NR_END));
 }  }
   
   /************************ivector *******************************/
 /*************** log-likelihood *************/  int *ivector(long nl,long nh)
 double func( double *x)  {
 {    int *v;
   int i, ii, j, k, mi, d, kk;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    if (!v) nrerror("allocation failure in ivector");
   double **out;    return v-nl+NR_END;
   double sw; /* Sum of weights */  }
   double lli; /* Individual log likelihood */  
   long ipmx;  /******************free ivector **************************/
   /*extern weight */  void free_ivector(int *v, long nl, long nh)
   /* We are differentiating ll according to initial status */  {
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    free((FREE_ARG)(v+nl-NR_END));
   /*for(i=1;i<imx;i++)  }
     printf(" %d\n",s[4][i]);  
   */  /************************lvector *******************************/
   cov[1]=1.;  long *lvector(long nl,long nh)
   {
   for(k=1; k<=nlstate; k++) ll[k]=0.;    long *v;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    if (!v) nrerror("allocation failure in ivector");
     for(mi=1; mi<= wav[i]-1; mi++){    return v-nl+NR_END;
       for (ii=1;ii<=nlstate+ndeath;ii++)  }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
       for(d=0; d<dh[mi][i]; d++){  /******************free lvector **************************/
         newm=savm;  void free_lvector(long *v, long nl, long nh)
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  {
         for (kk=1; kk<=cptcovage;kk++) {    free((FREE_ARG)(v+nl-NR_END));
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  }
         }  
          /******************* imatrix *******************************/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  int **imatrix(long nrl, long nrh, long ncl, long nch) 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         savm=oldm;  { 
         oldm=newm;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
            int **m; 
            
       } /* end mult */    /* allocate pointers to rows */ 
          m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    if (!m) nrerror("allocation failure 1 in matrix()"); 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    m += NR_END; 
       ipmx +=1;    m -= nrl; 
       sw += weight[i];    
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    
     } /* end of wave */    /* allocate rows and set pointers to them */ 
   } /* end of individual */    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    m[nrl] += NR_END; 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    m[nrl] -= ncl; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    
   return -l;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 }    
     /* return pointer to array of pointers to rows */ 
     return m; 
 /*********** Maximum Likelihood Estimation ***************/  } 
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  /****************** free_imatrix *************************/
 {  void free_imatrix(m,nrl,nrh,ncl,nch)
   int i,j, iter;        int **m;
   double **xi,*delti;        long nch,ncl,nrh,nrl; 
   double fret;       /* free an int matrix allocated by imatrix() */ 
   xi=matrix(1,npar,1,npar);  { 
   for (i=1;i<=npar;i++)    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     for (j=1;j<=npar;j++)    free((FREE_ARG) (m+nrl-NR_END)); 
       xi[i][j]=(i==j ? 1.0 : 0.0);  } 
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  {
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     double **m;
 }  
     m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 /**** Computes Hessian and covariance matrix ***/    if (!m) nrerror("allocation failure 1 in matrix()");
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    m += NR_END;
 {    m -= nrl;
   double  **a,**y,*x,pd;  
   double **hess;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   int i, j,jk;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   int *indx;    m[nrl] += NR_END;
     m[nrl] -= ncl;
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   void lubksb(double **a, int npar, int *indx, double b[]) ;    return m;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   hess=matrix(1,npar,1,npar);  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
      */
   printf("\nCalculation of the hessian matrix. Wait...\n");  }
   for (i=1;i<=npar;i++){  
     printf("%d",i);fflush(stdout);  /*************************free matrix ************************/
     hess[i][i]=hessii(p,ftolhess,i,delti);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     /*printf(" %f ",p[i]);*/  {
     /*printf(" %lf ",hess[i][i]);*/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   }    free((FREE_ARG)(m+nrl-NR_END));
    }
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++)  {  /******************* ma3x *******************************/
       if (j>i) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         printf(".%d%d",i,j);fflush(stdout);  {
         hess[i][j]=hessij(p,delti,i,j);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         hess[j][i]=hess[i][j];        double ***m;
         /*printf(" %lf ",hess[i][j]);*/  
       }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
   }    m += NR_END;
   printf("\n");    m -= nrl;
   
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   a=matrix(1,npar,1,npar);    m[nrl] += NR_END;
   y=matrix(1,npar,1,npar);    m[nrl] -= ncl;
   x=vector(1,npar);  
   indx=ivector(1,npar);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   ludcmp(a,npar,indx,&pd);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     m[nrl][ncl] += NR_END;
   for (j=1;j<=npar;j++) {    m[nrl][ncl] -= nll;
     for (i=1;i<=npar;i++) x[i]=0;    for (j=ncl+1; j<=nch; j++) 
     x[j]=1;      m[nrl][j]=m[nrl][j-1]+nlay;
     lubksb(a,npar,indx,x);    
     for (i=1;i<=npar;i++){    for (i=nrl+1; i<=nrh; i++) {
       matcov[i][j]=x[i];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     }      for (j=ncl+1; j<=nch; j++) 
   }        m[i][j]=m[i][j-1]+nlay;
     }
   printf("\n#Hessian matrix#\n");    return m; 
   for (i=1;i<=npar;i++) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     for (j=1;j<=npar;j++) {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       printf("%.3e ",hess[i][j]);    */
     }  }
     printf("\n");  
   }  /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   /* Recompute Inverse */  {
   for (i=1;i<=npar;i++)    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   ludcmp(a,npar,indx,&pd);    free((FREE_ARG)(m+nrl-NR_END));
   }
   /*  printf("\n#Hessian matrix recomputed#\n");  
   /*************** function subdirf ***********/
   for (j=1;j<=npar;j++) {  char *subdirf(char fileres[])
     for (i=1;i<=npar;i++) x[i]=0;  {
     x[j]=1;    /* Caution optionfilefiname is hidden */
     lubksb(a,npar,indx,x);    strcpy(tmpout,optionfilefiname);
     for (i=1;i<=npar;i++){    strcat(tmpout,"/"); /* Add to the right */
       y[i][j]=x[i];    strcat(tmpout,fileres);
       printf("%.3e ",y[i][j]);    return tmpout;
     }  }
     printf("\n");  
   }  /*************** function subdirf2 ***********/
   */  char *subdirf2(char fileres[], char *preop)
   {
   free_matrix(a,1,npar,1,npar);    
   free_matrix(y,1,npar,1,npar);    /* Caution optionfilefiname is hidden */
   free_vector(x,1,npar);    strcpy(tmpout,optionfilefiname);
   free_ivector(indx,1,npar);    strcat(tmpout,"/");
   free_matrix(hess,1,npar,1,npar);    strcat(tmpout,preop);
     strcat(tmpout,fileres);
     return tmpout;
 }  }
   
 /*************** hessian matrix ****************/  /*************** function subdirf3 ***********/
 double hessii( double x[], double delta, int theta, double delti[])  char *subdirf3(char fileres[], char *preop, char *preop2)
 {  {
   int i;    
   int l=1, lmax=20;    /* Caution optionfilefiname is hidden */
   double k1,k2;    strcpy(tmpout,optionfilefiname);
   double p2[NPARMAX+1];    strcat(tmpout,"/");
   double res;    strcat(tmpout,preop);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    strcat(tmpout,preop2);
   double fx;    strcat(tmpout,fileres);
   int k=0,kmax=10;    return tmpout;
   double l1;  }
   
   fx=func(x);  /***************** f1dim *************************/
   for (i=1;i<=npar;i++) p2[i]=x[i];  extern int ncom; 
   for(l=0 ; l <=lmax; l++){  extern double *pcom,*xicom;
     l1=pow(10,l);  extern double (*nrfunc)(double []); 
     delts=delt;   
     for(k=1 ; k <kmax; k=k+1){  double f1dim(double x) 
       delt = delta*(l1*k);  { 
       p2[theta]=x[theta] +delt;    int j; 
       k1=func(p2)-fx;    double f;
       p2[theta]=x[theta]-delt;    double *xt; 
       k2=func(p2)-fx;   
       /*res= (k1-2.0*fx+k2)/delt/delt; */    xt=vector(1,ncom); 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
          f=(*nrfunc)(xt); 
 #ifdef DEBUG    free_vector(xt,1,ncom); 
       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);    return f; 
 #endif  } 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  /*****************brent *************************/
         k=kmax;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       }  { 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    int iter; 
         k=kmax; l=lmax*10.;    double a,b,d,etemp;
       }    double fu,fv,fw,fx;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    double ftemp;
         delts=delt;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       }    double e=0.0; 
     }   
   }    a=(ax < cx ? ax : cx); 
   delti[theta]=delts;    b=(ax > cx ? ax : cx); 
   return res;    x=w=v=bx; 
      fw=fv=fx=(*f)(x); 
 }    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
 double hessij( double x[], double delti[], int thetai,int thetaj)      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   int i;      printf(".");fflush(stdout);
   int l=1, l1, lmax=20;      fprintf(ficlog,".");fflush(ficlog);
   double k1,k2,k3,k4,res,fx;  #ifdef DEBUG
   double p2[NPARMAX+1];      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);
   int k;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   fx=func(x);  #endif
   for (k=1; k<=2; k++) {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     for (i=1;i<=npar;i++) p2[i]=x[i];        *xmin=x; 
     p2[thetai]=x[thetai]+delti[thetai]/k;        return fx; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      } 
     k1=func(p2)-fx;      ftemp=fu;
        if (fabs(e) > tol1) { 
     p2[thetai]=x[thetai]+delti[thetai]/k;        r=(x-w)*(fx-fv); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        q=(x-v)*(fx-fw); 
     k2=func(p2)-fx;        p=(x-v)*q-(x-w)*r; 
          q=2.0*(q-r); 
     p2[thetai]=x[thetai]-delti[thetai]/k;        if (q > 0.0) p = -p; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        q=fabs(q); 
     k3=func(p2)-fx;        etemp=e; 
          e=d; 
     p2[thetai]=x[thetai]-delti[thetai]/k;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     k4=func(p2)-fx;        else { 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          d=p/q; 
 #ifdef DEBUG          u=x+d; 
     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 (u-a < tol2 || b-u < tol2) 
 #endif            d=SIGN(tol1,xm-x); 
   }        } 
   return res;      } else { 
 }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
 /************** Inverse of matrix **************/      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 void ludcmp(double **a, int n, int *indx, double *d)      fu=(*f)(u); 
 {      if (fu <= fx) { 
   int i,imax,j,k;        if (u >= x) a=x; else b=x; 
   double big,dum,sum,temp;        SHFT(v,w,x,u) 
   double *vv;          SHFT(fv,fw,fx,fu) 
            } else { 
   vv=vector(1,n);            if (u < x) a=u; else b=u; 
   *d=1.0;            if (fu <= fw || w == x) { 
   for (i=1;i<=n;i++) {              v=w; 
     big=0.0;              w=u; 
     for (j=1;j<=n;j++)              fv=fw; 
       if ((temp=fabs(a[i][j])) > big) big=temp;              fw=fu; 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");            } else if (fu <= fv || v == x || v == w) { 
     vv[i]=1.0/big;              v=u; 
   }              fv=fu; 
   for (j=1;j<=n;j++) {            } 
     for (i=1;i<j;i++) {          } 
       sum=a[i][j];    } 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    nrerror("Too many iterations in brent"); 
       a[i][j]=sum;    *xmin=x; 
     }    return fx; 
     big=0.0;  } 
     for (i=j;i<=n;i++) {  
       sum=a[i][j];  /****************** mnbrak ***********************/
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       a[i][j]=sum;              double (*func)(double)) 
       if ( (dum=vv[i]*fabs(sum)) >= big) {  { 
         big=dum;    double ulim,u,r,q, dum;
         imax=i;    double fu; 
       }   
     }    *fa=(*func)(*ax); 
     if (j != imax) {    *fb=(*func)(*bx); 
       for (k=1;k<=n;k++) {    if (*fb > *fa) { 
         dum=a[imax][k];      SHFT(dum,*ax,*bx,dum) 
         a[imax][k]=a[j][k];        SHFT(dum,*fb,*fa,dum) 
         a[j][k]=dum;        } 
       }    *cx=(*bx)+GOLD*(*bx-*ax); 
       *d = -(*d);    *fc=(*func)(*cx); 
       vv[imax]=vv[j];    while (*fb > *fc) { 
     }      r=(*bx-*ax)*(*fb-*fc); 
     indx[j]=imax;      q=(*bx-*cx)*(*fb-*fa); 
     if (a[j][j] == 0.0) a[j][j]=TINY;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     if (j != n) {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       dum=1.0/(a[j][j]);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      if ((*bx-u)*(u-*cx) > 0.0) { 
     }        fu=(*func)(u); 
   }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   free_vector(vv,1,n);  /* Doesn't work */        fu=(*func)(u); 
 ;        if (fu < *fc) { 
 }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
 void lubksb(double **a, int n, int *indx, double b[])            } 
 {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   int i,ii=0,ip,j;        u=ulim; 
   double sum;        fu=(*func)(u); 
        } else { 
   for (i=1;i<=n;i++) {        u=(*cx)+GOLD*(*cx-*bx); 
     ip=indx[i];        fu=(*func)(u); 
     sum=b[ip];      } 
     b[ip]=b[i];      SHFT(*ax,*bx,*cx,u) 
     if (ii)        SHFT(*fa,*fb,*fc,fu) 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        } 
     else if (sum) ii=i;  } 
     b[i]=sum;  
   }  /*************** linmin ************************/
   for (i=n;i>=1;i--) {  
     sum=b[i];  int ncom; 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  double *pcom,*xicom;
     b[i]=sum/a[i][i];  double (*nrfunc)(double []); 
   }   
 }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   { 
 /************ Frequencies ********************/    double brent(double ax, double bx, double cx, 
 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 (*f)(double), double tol, double *xmin); 
 {  /* Some frequencies */    double f1dim(double x); 
      void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;                double *fc, double (*func)(double)); 
   double ***freq; /* Frequencies */    int j; 
   double *pp;    double xx,xmin,bx,ax; 
   double pos, k2, dateintsum=0,k2cpt=0;    double fx,fb,fa;
   FILE *ficresp;   
   char fileresp[FILENAMELENGTH];    ncom=n; 
     pcom=vector(1,n); 
   pp=vector(1,nlstate);    xicom=vector(1,n); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    nrfunc=func; 
   strcpy(fileresp,"p");    for (j=1;j<=n;j++) { 
   strcat(fileresp,fileres);      pcom[j]=p[j]; 
   if((ficresp=fopen(fileresp,"w"))==NULL) {      xicom[j]=xi[j]; 
     printf("Problem with prevalence resultfile: %s\n", fileresp);    } 
     exit(0);    ax=0.0; 
   }    xx=1.0; 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   j1=0;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
   j=cptcoveff;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
   for(k1=1; k1<=j;k1++){    for (j=1;j<=n;j++) { 
    for(i1=1; i1<=ncodemax[k1];i1++){      xi[j] *= xmin; 
        j1++;      p[j] += xi[j]; 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    } 
          scanf("%d", i);*/    free_vector(xicom,1,n); 
         for (i=-1; i<=nlstate+ndeath; i++)      free_vector(pcom,1,n); 
          for (jk=-1; jk<=nlstate+ndeath; jk++)    } 
            for(m=agemin; m <= agemax+3; m++)  
              freq[i][jk][m]=0;  char *asc_diff_time(long time_sec, char ascdiff[])
   {
         dateintsum=0;    long sec_left, days, hours, minutes;
         k2cpt=0;    days = (time_sec) / (60*60*24);
        for (i=1; i<=imx; i++) {    sec_left = (time_sec) % (60*60*24);
          bool=1;    hours = (sec_left) / (60*60) ;
          if  (cptcovn>0) {    sec_left = (sec_left) %(60*60);
            for (z1=1; z1<=cptcoveff; z1++)    minutes = (sec_left) /60;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    sec_left = (sec_left) % (60);
                bool=0;    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
          }    return ascdiff;
          if (bool==1) {  }
            for(m=firstpass; m<=lastpass; m++){  
              k2=anint[m][i]+(mint[m][i]/12.);  /*************** powell ************************/
              if ((k2>=dateprev1) && (k2<=dateprev2)) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
                if(agev[m][i]==0) agev[m][i]=agemax+1;              double (*func)(double [])) 
                if(agev[m][i]==1) agev[m][i]=agemax+2;  { 
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    void linmin(double p[], double xi[], int n, double *fret, 
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];                double (*func)(double [])); 
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    int i,ibig,j; 
                  dateintsum=dateintsum+k2;    double del,t,*pt,*ptt,*xit;
                  k2cpt++;    double fp,fptt;
                }    double *xits;
     int niterf, itmp;
              }  
            }    pt=vector(1,n); 
          }    ptt=vector(1,n); 
        }    xit=vector(1,n); 
         if  (cptcovn>0) {    xits=vector(1,n); 
          fprintf(ficresp, "\n#********** Variable ");    *fret=(*func)(p); 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for (j=1;j<=n;j++) pt[j]=p[j]; 
        fprintf(ficresp, "**********\n#");    for (*iter=1;;++(*iter)) { 
         }      fp=(*fret); 
        for(i=1; i<=nlstate;i++)      ibig=0; 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      del=0.0; 
        fprintf(ficresp, "\n");      last_time=curr_time;
              (void) gettimeofday(&curr_time,&tzp);
   for(i=(int)agemin; i <= (int)agemax+3; i++){      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
     if(i==(int)agemax+3)      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
       printf("Total");  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
     else     for (i=1;i<=n;i++) {
       printf("Age %d", i);        printf(" %d %.12f",i, p[i]);
     for(jk=1; jk <=nlstate ; jk++){        fprintf(ficlog," %d %.12lf",i, p[i]);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        fprintf(ficrespow," %.12lf", p[i]);
         pp[jk] += freq[jk][m][i];      }
     }      printf("\n");
     for(jk=1; jk <=nlstate ; jk++){      fprintf(ficlog,"\n");
       for(m=-1, pos=0; m <=0 ; m++)      fprintf(ficrespow,"\n");fflush(ficrespow);
         pos += freq[jk][m][i];      if(*iter <=3){
       if(pp[jk]>=1.e-10)        tm = *localtime(&curr_time.tv_sec);
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        strcpy(strcurr,asctime(&tm));
       else  /*       asctime_r(&tm,strcurr); */
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        forecast_time=curr_time; 
     }        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
      for(jk=1; jk <=nlstate ; jk++){          strcurr[itmp-1]='\0';
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         pp[jk] += freq[jk][m][i];        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
      }        for(niterf=10;niterf<=30;niterf+=10){
           forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     for(jk=1,pos=0; jk <=nlstate ; jk++)          tmf = *localtime(&forecast_time.tv_sec);
       pos += pp[jk];  /*      asctime_r(&tmf,strfor); */
     for(jk=1; jk <=nlstate ; jk++){          strcpy(strfor,asctime(&tmf));
       if(pos>=1.e-5)          itmp = strlen(strfor);
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          if(strfor[itmp-1]=='\n')
       else          strfor[itmp-1]='\0';
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       if( i <= (int) agemax){          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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
         if(pos>=1.e-5){        }
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      }
           probs[i][jk][j1]= pp[jk]/pos;      for (i=1;i<=n;i++) { 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         }        fptt=(*fret); 
       else  #ifdef DEBUG
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        printf("fret=%lf \n",*fret);
       }        fprintf(ficlog,"fret=%lf \n",*fret);
     }  #endif
     for(jk=-1; jk <=nlstate+ndeath; jk++)        printf("%d",i);fflush(stdout);
       for(m=-1; m <=nlstate+ndeath; m++)        fprintf(ficlog,"%d",i);fflush(ficlog);
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        linmin(p,xit,n,fret,func); 
     if(i <= (int) agemax)        if (fabs(fptt-(*fret)) > del) { 
       fprintf(ficresp,"\n");          del=fabs(fptt-(*fret)); 
     printf("\n");          ibig=i; 
     }        } 
     }  #ifdef DEBUG
  }        printf("%d %.12e",i,(*fret));
   dateintmean=dateintsum/k2cpt;        fprintf(ficlog,"%d %.12e",i,(*fret));
          for (j=1;j<=n;j++) {
   fclose(ficresp);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          printf(" x(%d)=%.12e",j,xit[j]);
   free_vector(pp,1,nlstate);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
   /* End of Freq */        for(j=1;j<=n;j++) {
 }          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
 /************ Prevalence ********************/        }
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)        printf("\n");
 {  /* Some frequencies */        fprintf(ficlog,"\n");
    #endif
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      } 
   double ***freq; /* Frequencies */      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   double *pp;  #ifdef DEBUG
   double pos, k2;        int k[2],l;
         k[0]=1;
   pp=vector(1,nlstate);        k[1]=-1;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        printf("Max: %.12e",(*func)(p));
          fprintf(ficlog,"Max: %.12e",(*func)(p));
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        for (j=1;j<=n;j++) {
   j1=0;          printf(" %.12e",p[j]);
            fprintf(ficlog," %.12e",p[j]);
   j=cptcoveff;        }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        printf("\n");
          fprintf(ficlog,"\n");
  for(k1=1; k1<=j;k1++){        for(l=0;l<=1;l++) {
     for(i1=1; i1<=ncodemax[k1];i1++){          for (j=1;j<=n;j++) {
       j1++;            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=-1; i<=nlstate+ndeath; 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+ndeath; jk++)            }
           for(m=agemin; m <= agemax+3; m++)          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
             freq[i][jk][m]=0;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
              }
       for (i=1; i<=imx; i++) {  #endif
         bool=1;  
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)        free_vector(xit,1,n); 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        free_vector(xits,1,n); 
               bool=0;        free_vector(ptt,1,n); 
         }        free_vector(pt,1,n); 
         if (bool==1) {        return; 
           for(m=firstpass; m<=lastpass; m++){      } 
             k2=anint[m][i]+(mint[m][i]/12.);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      for (j=1;j<=n;j++) { 
               if(agev[m][i]==0) agev[m][i]=agemax+1;        ptt[j]=2.0*p[j]-pt[j]; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;        xit[j]=p[j]-pt[j]; 
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        pt[j]=p[j]; 
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];        } 
             }      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(i=(int)agemin; i <= (int)agemax+3; i++){          for (j=1;j<=n;j++) { 
           for(jk=1; jk <=nlstate ; jk++){            xi[j][ibig]=xi[j][n]; 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            xi[j][n]=xit[j]; 
               pp[jk] += freq[jk][m][i];          }
           }  #ifdef DEBUG
           for(jk=1; jk <=nlstate ; jk++){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
             for(m=-1, pos=0; m <=0 ; m++)          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
             pos += freq[jk][m][i];          for(j=1;j<=n;j++){
         }            printf(" %.12e",xit[j]);
                    fprintf(ficlog," %.12e",xit[j]);
          for(jk=1; jk <=nlstate ; jk++){          }
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          printf("\n");
              pp[jk] += freq[jk][m][i];          fprintf(ficlog,"\n");
          }  #endif
                  }
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      } 
     } 
          for(jk=1; jk <=nlstate ; jk++){            } 
            if( i <= (int) agemax){  
              if(pos>=1.e-5){  /**** Prevalence limit (stable or period prevalence)  ****************/
                probs[i][jk][j1]= pp[jk]/pos;  
              }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
            }  {
          }    /* 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 i, ii,j,k;
   }    double min, max, maxmin, maxmax,sumnew=0.;
      /* double **matprod2(); */ /* test */
      double **out, cov[NCOVMAX+1], **pmij();
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double **newm;
   free_vector(pp,1,nlstate);    double agefin, delaymax=50 ; /* Max number of years to converge */
    
 }  /* End of Freq */    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
 /************* Waves Concatenation ***************/        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {     cov[1]=1.;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.   
      Death is a valid wave (if date is known).   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      newm=savm;
      and mw[mi+1][i]. dh depends on stepm.      /* Covariates have to be included here again */
      */      cov[2]=agefin;
       
   int i, mi, m;      for (k=1; k<=cptcovn;k++) {
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
      double sum=0., jmean=0.;*/        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
       }
   int j, k=0,jk, ju, jl;      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   double sum=0.;      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
   jmin=1e+5;      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
   jmax=-1;      
   jmean=0.;      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   for(i=1; i<=imx; i++){      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     mi=0;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     m=firstpass;      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     while(s[m][i] <= nlstate){      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
       if(s[m][i]>=1)      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
         mw[++mi][i]=m;      
       if(m >=lastpass)      savm=oldm;
         break;      oldm=newm;
       else      maxmax=0.;
         m++;      for(j=1;j<=nlstate;j++){
     }/* end while */        min=1.;
     if (s[m][i] > nlstate){        max=0.;
       mi++;     /* Death is another wave */        for(i=1; i<=nlstate; i++) {
       /* if(mi==0)  never been interviewed correctly before death */          sumnew=0;
          /* Only death is a correct wave */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       mw[mi][i]=m;          prlim[i][j]= newm[i][j]/(1-sumnew);
     }          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
           max=FMAX(max,prlim[i][j]);
     wav[i]=mi;          min=FMIN(min,prlim[i][j]);
     if(mi==0)        }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        maxmin=max-min;
   }        maxmax=FMAX(maxmax,maxmin);
       }
   for(i=1; i<=imx; i++){      if(maxmax < ftolpl){
     for(mi=1; mi<wav[i];mi++){        return prlim;
       if (stepm <=0)      }
         dh[mi][i]=1;    }
       else{  }
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {  /*************** transition probabilities ***************/ 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j==0) j=1;  /* Survives at least one month after exam */  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
           k=k+1;  {
           if (j >= jmax) jmax=j;    /* According to parameters values stored in x and the covariate's values stored in cov,
           if (j <= jmin) jmin=j;       computes the probability to be observed in state j being in state i by appying the
           sum=sum+j;       model to the ncovmodel covariates (including constant and age).
           /* if (j<10) printf("j=%d num=%d ",j,i); */       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
           }       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
         }       ncth covariate in the global vector x is given by the formula:
         else{       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
           k=k+1;       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
           if (j >= jmax) jmax=j;       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
           else if (j <= jmin)jmin=j;       Outputs ps[i][j] the probability to be observed in j being in j according to
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
           sum=sum+j;    */
         }    double s1, lnpijopii;
         jk= j/stepm;    /*double t34;*/
         jl= j -jk*stepm;    int i,j,j1, nc, ii, jj;
         ju= j -(jk+1)*stepm;  
         if(jl <= -ju)      for(i=1; i<= nlstate; i++){
           dh[mi][i]=jk;        for(j=1; j<i;j++){
         else          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           dh[mi][i]=jk+1;            /*lnpijopii += param[i][j][nc]*cov[nc];*/
         if(dh[mi][i]==0)            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
           dh[mi][i]=1; /* At least one step */  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       }          }
     }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   }  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   jmean=sum/k;        }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        for(j=i+1; j<=nlstate+ndeath;j++){
  }          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
 /*********** Tricode ****************************/            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
 void tricode(int *Tvar, int **nbcode, int imx)            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
 {  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
   int Ndum[20],ij=1, k, j, i;          }
   int cptcode=0;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   cptcoveff=0;        }
        }
   for (k=0; k<19; k++) Ndum[k]=0;      
   for (k=1; k<=7; k++) ncodemax[k]=0;      for(i=1; i<= nlstate; i++){
         s1=0;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        for(j=1; j<i; j++){
     for (i=1; i<=imx; i++) {          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       ij=(int)(covar[Tvar[j]][i]);          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       Ndum[ij]++;        }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        for(j=i+1; j<=nlstate+ndeath; j++){
       if (ij > cptcode) cptcode=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); */
         }
     for (i=0; i<=cptcode; i++) {        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       if(Ndum[i]!=0) ncodemax[j]++;        ps[i][i]=1./(s1+1.);
     }        /* Computing other pijs */
     ij=1;        for(j=1; j<i; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
     for (i=1; i<=ncodemax[j]; i++) {          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for (k=0; k<=19; k++) {        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         if (Ndum[k] != 0) {      } /* end i */
           nbcode[Tvar[j]][ij]=k;      
           ij++;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         }        for(jj=1; jj<= nlstate+ndeath; jj++){
         if (ij > ncodemax[j]) break;          ps[ii][jj]=0;
       }            ps[ii][ii]=1;
     }        }
   }        }
       
  for (k=0; k<19; k++) Ndum[k]=0;      
       /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
  for (i=1; i<=ncovmodel-2; i++) {      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
       ij=Tvar[i];      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       Ndum[ij]++;      /*   } */
     }      /*   printf("\n "); */
       /* } */
  ij=1;      /* printf("\n ");printf("%lf ",cov[2]);*/
  for (i=1; i<=10; i++) {      /*
    if((Ndum[i]!=0) && (i<=ncov)){        for(i=1; i<= npar; i++) printf("%f ",x[i]);
      Tvaraff[ij]=i;        goto end;*/
      ij++;      return ps;
    }  }
  }  
    /**************** Product of 2 matrices ******************/
     cptcoveff=ij-1;  
 }  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   {
 /*********** Health Expectancies ****************/    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
        b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    /* in, b, out are matrice of pointers which should have been initialized 
 {       before: only the contents of out is modified. The function returns
   /* Health expectancies */       a pointer to pointers identical to out */
   int i, j, nhstepm, hstepm, h;    int i, j, k;
   double age, agelim,hf;    for(i=nrl; i<= nrh; i++)
   double ***p3mat;      for(k=ncolol; k<=ncoloh; k++){
          out[i][k]=0.;
   fprintf(ficreseij,"# Health expectancies\n");        for(j=ncl; j<=nch; j++)
   fprintf(ficreseij,"# Age");          out[i][k] +=in[i][j]*b[j][k];
   for(i=1; i<=nlstate;i++)      }
     for(j=1; j<=nlstate;j++)    return out;
       fprintf(ficreseij," %1d-%1d",i,j);  }
   fprintf(ficreseij,"\n");  
   
   hstepm=1*YEARM; /*  Every j years of age (in month) */  /************* Higher Matrix Product ***************/
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   agelim=AGESUP;  {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* Computes the transition matrix starting at age 'age' over 
     /* nhstepm age range expressed in number of stepm */       'nhstepm*hstepm*stepm' months (i.e. until
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     /* Typically if 20 years = 20*12/6=40 stepm */       nhstepm*hstepm matrices. 
     if (stepm >= YEARM) hstepm=1;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */       (typically every 2 years instead of every month which is too big 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       for the memory).
     /* Computed by stepm unit matrices, product of hstepm matrices, stored       Model is determined by parameters x and covariates have to be 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */       included manually here. 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    
        */
   
     for(i=1; i<=nlstate;i++)    int i, j, d, h, k;
       for(j=1; j<=nlstate;j++)    double **out, cov[NCOVMAX+1];
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    double **newm;
           eij[i][j][(int)age] +=p3mat[i][j][h];  
         }    /* Hstepm could be zero and should return the unit matrix */
        for (i=1;i<=nlstate+ndeath;i++)
     hf=1;      for (j=1;j<=nlstate+ndeath;j++){
     if (stepm >= YEARM) hf=stepm/YEARM;        oldm[i][j]=(i==j ? 1.0 : 0.0);
     fprintf(ficreseij,"%.0f",age );        po[i][j][0]=(i==j ? 1.0 : 0.0);
     for(i=1; i<=nlstate;i++)      }
       for(j=1; j<=nlstate;j++){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);    for(h=1; h <=nhstepm; h++){
       }      for(d=1; d <=hstepm; d++){
     fprintf(ficreseij,"\n");        newm=savm;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* Covariates have to be included here again */
   }        cov[1]=1.;
 }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) 
 /************ Variance ******************/          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 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 (k=1; k<=cptcovage;k++)
 {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /* Variance of health expectancies */        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double **newm;  
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm, h;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   int k, cptcode;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   double *xp;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   double **gp, **gm;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   double ***gradg, ***trgradg;        savm=oldm;
   double ***p3mat;        oldm=newm;
   double age,agelim;      }
   int theta;      for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
    fprintf(ficresvij,"# Covariances of life expectancies\n");          po[i][j][h]=newm[i][j];
   fprintf(ficresvij,"# Age");          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   for(i=1; i<=nlstate;i++)        }
     for(j=1; j<=nlstate;j++)      /*printf("h=%d ",h);*/
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    } /* end h */
   fprintf(ficresvij,"\n");  /*     printf("\n H=%d \n",h); */
     return po;
   xp=vector(1,npar);  }
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);  
    /*************** log-likelihood *************/
   hstepm=1*YEARM; /* Every year of age */  double func( double *x)
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  {
   agelim = AGESUP;    int i, ii, j, k, mi, d, kk;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double **out;
     if (stepm >= YEARM) hstepm=1;    double sw; /* Sum of weights */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double lli; /* Individual log likelihood */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int s1, s2;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    double bbh, survp;
     gp=matrix(0,nhstepm,1,nlstate);    long ipmx;
     gm=matrix(0,nhstepm,1,nlstate);    /*extern weight */
     /* We are differentiating ll according to initial status */
     for(theta=1; theta <=npar; theta++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       for(i=1; i<=npar; i++){ /* Computes gradient */    /*for(i=1;i<imx;i++) 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      printf(" %d\n",s[4][i]);
       }    */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      cov[1]=1.;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)    if(mle==1){
           prlim[i][i]=probs[(int)age][i][ij];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }        /* Computes the values of the ncovmodel covariates of the model
                 depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
       for(j=1; j<= nlstate; j++){           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
         for(h=0; h<=nhstepm; h++){           to be observed in j being in i according to the model.
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)         */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
         }          cov[2+k]=covar[Tvar[k]][i];
       }        }
            /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
       for(i=1; i<=npar; i++) /* Computes gradient */           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);           has been calculated etc */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          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 (j=1;j<=nlstate+ndeath;j++){
       if (popbased==1) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(i=1; i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           prlim[i][i]=probs[(int)age][i][ij];            }
       }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
       for(j=1; j<= nlstate; j++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for(h=0; h<=nhstepm; h++){            for (kk=1; kk<=cptcovage;kk++) {
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            }
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
       for(j=1; j<= nlstate; j++)            oldm=newm;
         for(h=0; h<=nhstepm; h++){          } /* end mult */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        
         }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     } /* End theta */          /* 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 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);           * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
     for(h=0; h<=nhstepm; h++)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       for(j=1; j<=nlstate;j++)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         for(theta=1; theta <=npar; theta++)           * probability in order to take into account the bias as a fraction of the way
           trgradg[h][j][theta]=gradg[h][theta][j];           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
     for(i=1;i<=nlstate;i++)           * For stepm=1 the results are the same as for previous versions of Imach.
       for(j=1;j<=nlstate;j++)           * For stepm > 1 the results are less biased than in previous versions. 
         vareij[i][j][(int)age] =0.;           */
     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];          /* 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 
     h=1;               then the contribution to the likelihood is the probability to 
     if (stepm >= YEARM) h=stepm/YEARM;               die between last step unit time and current  step unit time, 
     fprintf(ficresvij,"%.0f ",age );               which is also equal to probability to die before dh 
     for(i=1; i<=nlstate;i++)               minus probability to die before dh-stepm . 
       for(j=1; j<=nlstate;j++){               In version up to 0.92 likelihood was computed
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          as if date of death was unknown. Death was treated as any other
       }          health state: the date of the interview describes the actual state
     fprintf(ficresvij,"\n");          and not the date of a change in health state. The former idea was
     free_matrix(gp,0,nhstepm,1,nlstate);          to consider that at each interview the state was recorded
     free_matrix(gm,0,nhstepm,1,nlstate);          (healthy, disable or death) and IMaCh was corrected; but when we
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          introduced the exact date of death then we should have modified
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          the contribution of an exact death to the likelihood. This new
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          contribution is smaller and very dependent of the step unit
   } /* End age */          stepm. It is no more the probability to die between last interview
            and month of death but the probability to survive from last
   free_vector(xp,1,npar);          interview up to one month before death multiplied by the
   free_matrix(doldm,1,nlstate,1,npar);          probability to die within a month. Thanks to Chris
   free_matrix(dnewm,1,nlstate,1,nlstate);          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%
           lower mortality.
 /************ 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)            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);*/          } else if  (s2==-2) {
   double **newm;            for (j=1,survp=0. ; j<=nlstate; j++) 
   double **dnewm,**doldm;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   int i, j, nhstepm, hstepm;            /*survp += out[s1][j]; */
   int k, cptcode;            lli= log(survp);
   double *xp;          }
   double *gp, *gm;          
   double **gradg, **trgradg;          else if  (s2==-4) { 
   double age,agelim;            for (j=3,survp=0. ; j<=nlstate; j++)  
   int theta;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                lli= log(survp); 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          } 
   fprintf(ficresvpl,"# Age");  
   for(i=1; i<=nlstate;i++)          else if  (s2==-5) { 
       fprintf(ficresvpl," %1d-%1d",i,i);            for (j=1,survp=0. ; j<=2; j++)  
   fprintf(ficresvpl,"\n");              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
   xp=vector(1,npar);          } 
   dnewm=matrix(1,nlstate,1,npar);          
   doldm=matrix(1,nlstate,1,nlstate);          else{
              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   hstepm=1*YEARM; /* Every year of age */            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          } 
   agelim = AGESUP;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          /*if(lli ==000.0)*/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     if (stepm >= YEARM) hstepm=1;          ipmx +=1;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          sw += weight[i];
     gradg=matrix(1,npar,1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     gp=vector(1,nlstate);        } /* end of wave */
     gm=vector(1,nlstate);      } /* end of individual */
     }  else if(mle==2){
     for(theta=1; theta <=npar; theta++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(i=1; i<=npar; i++){ /* Computes gradient */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            for (j=1;j<=nlstate+ndeath;j++){
       for(i=1;i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         gp[i] = prlim[i][i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                }
       for(i=1; i<=npar; i++) /* Computes gradient */          for(d=0; d<=dh[mi][i]; d++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            newm=savm;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(i=1;i<=nlstate;i++)            for (kk=1; kk<=cptcovage;kk++) {
         gm[i] = prlim[i][i];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
       for(i=1;i<=nlstate;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     } /* End theta */            savm=oldm;
             oldm=newm;
     trgradg =matrix(1,nlstate,1,npar);          } /* end mult */
         
     for(j=1; j<=nlstate;j++)          s1=s[mw[mi][i]][i];
       for(theta=1; theta <=npar; theta++)          s2=s[mw[mi+1][i]][i];
         trgradg[j][theta]=gradg[theta][j];          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     for(i=1;i<=nlstate;i++)          ipmx +=1;
       varpl[i][(int)age] =0.;          sw += weight[i];
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        } /* end of wave */
     for(i=1;i<=nlstate;i++)      } /* end of individual */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fprintf(ficresvpl,"%.0f ",age );        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for(i=1; i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          for (ii=1;ii<=nlstate+ndeath;ii++)
     fprintf(ficresvpl,"\n");            for (j=1;j<=nlstate+ndeath;j++){
     free_vector(gp,1,nlstate);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_vector(gm,1,nlstate);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_matrix(gradg,1,npar,1,nlstate);            }
     free_matrix(trgradg,1,nlstate,1,npar);          for(d=0; d<dh[mi][i]; d++){
   } /* End age */            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_vector(xp,1,npar);            for (kk=1; kk<=cptcovage;kk++) {
   free_matrix(doldm,1,nlstate,1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_matrix(dnewm,1,nlstate,1,nlstate);            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
 /************ Variance of one-step probabilities  ******************/            oldm=newm;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)          } /* end mult */
 {        
   int i, j;          s1=s[mw[mi][i]][i];
   int k=0, cptcode;          s2=s[mw[mi+1][i]][i];
   double **dnewm,**doldm;          bbh=(double)bh[mi][i]/(double)stepm; 
   double *xp;          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 *gp, *gm;          ipmx +=1;
   double **gradg, **trgradg;          sw += weight[i];
   double age,agelim, cov[NCOVMAX];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int theta;        } /* end of wave */
   char fileresprob[FILENAMELENGTH];      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
   strcpy(fileresprob,"prob");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcat(fileresprob,fileres);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        for(mi=1; mi<= wav[i]-1; mi++){
     printf("Problem with resultfile: %s\n", fileresprob);          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   xp=vector(1,npar);          for(d=0; d<dh[mi][i]; d++){
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            newm=savm;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
   cov[1]=1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for (age=bage; age<=fage; age ++){            }
     cov[2]=age;          
     gradg=matrix(1,npar,1,9);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     trgradg=matrix(1,9,1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            savm=oldm;
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            oldm=newm;
              } /* end mult */
     for(theta=1; theta <=npar; theta++){        
       for(i=1; i<=npar; i++)          s1=s[mw[mi][i]][i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          s2=s[mw[mi+1][i]][i];
                if( s2 > nlstate){ 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            lli=log(out[s1][s2] - savm[s1][s2]);
              }else{
       k=0;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       for(i=1; i<= (nlstate+ndeath); i++){          }
         for(j=1; j<=(nlstate+ndeath);j++){          ipmx +=1;
            k=k+1;          sw += weight[i];
           gp[k]=pmmij[i][j];          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 */
       } /* end of individual */
       for(i=1; i<=npar; i++)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      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++){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
       k=0;            for (j=1;j<=nlstate+ndeath;j++){
       for(i=1; i<=(nlstate+ndeath); i++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(j=1; j<=(nlstate+ndeath);j++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           k=k+1;            }
           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 (kk=1; kk<=cptcovage;kk++) {
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              }
     }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(theta=1; theta <=npar; theta++)            savm=oldm;
       trgradg[j][theta]=gradg[theta][j];            oldm=newm;
            } /* end mult */
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
      pmij(pmmij,cov,ncovmodel,x,nlstate);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
      k=0;          sw += weight[i];
      for(i=1; i<=(nlstate+ndeath); i++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
        for(j=1; j<=(nlstate+ndeath);j++){          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
          k=k+1;        } /* end of wave */
          gm[k]=pmmij[i][j];      } /* end of individual */
         }    } /* End of if */
      }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
          /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      /*printf("\n%d ",(int)age);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    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 */
     int i, ii, j, k, mi, d, kk;
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    double **out;
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    double lli; /* Individual log likelihood */
   }    double llt;
     int s1, s2;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    double bbh, survp;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    /*extern weight */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /* We are differentiating ll according to initial status */
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 }    /*for(i=1;i<imx;i++) 
  free_vector(xp,1,npar);      printf(" %d\n",s[4][i]);
 fclose(ficresprob);    */
  exit(0);    cov[1]=1.;
 }  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
 /******************* 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 optionfile[],char optionfilehtm[] ){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int jj1, k1, i1, cpt;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   FILE *fichtm;      for(mi=1; mi<= wav[i]-1; mi++){
   /*char optionfilehtm[FILENAMELENGTH];*/        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
   strcpy(optionfilehtm,optionfile);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcat(optionfilehtm,".htm");            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          }
     printf("Problem with %s \n",optionfilehtm), exit(0);        for(d=0; d<dh[mi][i]; d++){
   }          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">          for (kk=1; kk<=cptcovage;kk++) {
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }
 Total number of observations=%d <br>          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 <hr  size=\"2\" color=\"#EC5E5E\">                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 <li>Outputs files<br><br>\n          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          savm=oldm;
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>          oldm=newm;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        } /* end mult */
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>        
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>        s1=s[mw[mi][i]][i];
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>        s2=s[mw[mi+1][i]][i];
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>        bbh=(double)bh[mi][i]/(double)stepm; 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>        /* bias is positive if real duration
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>         * is higher than the multiple of stepm and negative otherwise.
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);         */
          if( s2 > nlstate && (mle <5) ){  /* Jackson */
 fprintf(fichtm," <li>Graphs</li><p>");          lli=log(out[s1][s2] - savm[s1][s2]);
         } else if  (s2==-2) {
  m=cptcoveff;          for (j=1,survp=0. ; j<=nlstate; j++) 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);
  jj1=0;        }else if (mle==1){
  for(k1=1; k1<=m;k1++){          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
    for(i1=1; i1<=ncodemax[k1];i1++){        } else if(mle==2){
        jj1++;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
        if (cptcovn > 0) {        } else if(mle==3){  /* exponential inter-extrapolation */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
          for (cpt=1; cpt<=cptcoveff;cpt++)        } else if (mle==4){  /* mle=4 no inter-extrapolation */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          lli=log(out[s1][s2]); /* Original formula */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        } else{  /* mle=0 back to 1 */
        }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          /*lli=log(out[s1][s2]); */ /* Original formula */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            } /* End of if */
        for(cpt=1; cpt<nlstate;cpt++){        ipmx +=1;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        sw += weight[i];
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
        }        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     for(cpt=1; cpt<=nlstate;cpt++) {        if(globpr){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
 interval) in state (%d): v%s%d%d.gif <br>   %11.6f %11.6f %11.6f ", \
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                    num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
      }                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
      for(cpt=1; cpt<=nlstate;cpt++) {          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>            llt +=ll[k]*gipmx/gsw;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
      }          }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          fprintf(ficresilk," %10.6f\n", -llt);
 health expectancies in states (1) and (2): e%s%d.gif<br>        }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      } /* end of wave */
 fprintf(fichtm,"\n</body>");    } /* end of individual */
    }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
    }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 fclose(fichtm);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
 }    if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
 /******************* Gnuplot file **************/      gsw=sw;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemax, double fage , char pathc[], double p[]){    }
     return -l;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;  }
   
   strcpy(optionfilegnuplot,optionfilefiname);  
   strcat(optionfilegnuplot,".plt");  /*************** function likelione ***********/
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     printf("Problem with file %s",optionfilegnuplot);  {
   }    /* This routine should help understanding what is done with 
        the selection of individuals/waves and
 #ifdef windows       to check the exact contribution to the likelihood.
     fprintf(ficgp,"cd \"%s\" \n",pathc);       Plotting could be done.
 #endif     */
 m=pow(2,cptcoveff);    int k;
    
  /* 1eme*/    if(*globpri !=0){ /* Just counts and sums, no printings */
   for (cpt=1; cpt<= nlstate ; cpt ++) {      strcpy(fileresilk,"ilk"); 
    for (k1=1; k1<= m ; k1 ++) {      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
 #ifdef windows        printf("Problem with resultfile: %s\n", fileresilk);
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
 #endif      }
 #ifdef unix      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");
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
 #endif      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(k=1; k<=nlstate; k++) 
 for (i=1; i<= nlstate ; i ++) {        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   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);    *fretone=(*funcone)(p);
     for (i=1; i<= nlstate ; i ++) {    if(*globpri !=0){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      fclose(ficresilk);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
 }      fflush(fichtm); 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    } 
      for (i=1; i<= nlstate ; i ++) {    return;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  /*********** Maximum Likelihood Estimation ***************/
 #ifdef unix  
 fprintf(ficgp,"\nset ter gif small size 400,300");  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 #endif  {
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    int i,j, iter;
    }    double **xi;
   }    double fret;
   /*2 eme*/    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
   for (k1=1; k1<= m ; k1 ++) {    xi=matrix(1,npar,1,npar);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    for (i=1;i<=npar;i++)
          for (j=1;j<=npar;j++)
     for (i=1; i<= nlstate+1 ; i ++) {        xi[i][j]=(i==j ? 1.0 : 0.0);
       k=2*i;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    strcpy(filerespow,"pow"); 
       for (j=1; j<= nlstate+1 ; j ++) {    strcat(filerespow,fileres);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");      printf("Problem with resultfile: %s\n", filerespow);
 }        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    for (i=1;i<=nlstate;i++)
       for (j=1; j<= nlstate+1 ; j ++) {      for(j=1;j<=nlstate+ndeath;j++)
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
         else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficrespow,"\n");
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");    powell(p,xi,npar,ftol,&iter,&fret,func);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {    free_matrix(xi,1,npar,1,npar);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fclose(ficrespow);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
 }      fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       else fprintf(ficgp,"\" t\"\" w l 0,");  
     }  }
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  
   }  /**** Computes Hessian and covariance matrix ***/
    void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   /*3eme*/  {
     double  **a,**y,*x,pd;
   for (k1=1; k1<= m ; k1 ++) {    double **hess;
     for (cpt=1; cpt<= nlstate ; cpt ++) {    int i, j,jk;
       k=2+nlstate*(cpt-1);    int *indx;
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);  
       for (i=1; i< nlstate ; i ++) {    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
         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);    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[]) ;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    void ludcmp(double **a, int npar, int *indx, double *d) ;
     }    double gompertz(double p[]);
     }    hess=matrix(1,npar,1,npar);
    
   /* CV preval stat */    printf("\nCalculation of the hessian matrix. Wait...\n");
     for (k1=1; k1<= m ; k1 ++) {    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (cpt=1; cpt<nlstate ; cpt ++) {    for (i=1;i<=npar;i++){
       k=3;      printf("%d",i);fflush(stdout);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);      fprintf(ficlog,"%d",i);fflush(ficlog);
      
       for (i=1; i< nlstate ; i ++)       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
         fprintf(ficgp,"+$%d",k+i+1);      
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      /*  printf(" %f ",p[i]);
                printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       l=3+(nlstate+ndeath)*cpt;    }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    
       for (i=1; i< nlstate ; i ++) {    for (i=1;i<=npar;i++) {
         l=3+(nlstate+ndeath)*cpt;      for (j=1;j<=npar;j++)  {
         fprintf(ficgp,"+$%d",l+i+1);        if (j>i) { 
       }          printf(".%d%d",i,j);fflush(stdout);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          hess[i][j]=hessij(p,delti,i,j,func,npar);
     }          
   }            hess[j][i]=hess[i][j];    
            /*printf(" %lf ",hess[i][j]);*/
   /* proba elementaires */        }
    for(i=1,jk=1; i <=nlstate; i++){      }
     for(k=1; k <=(nlstate+ndeath); k++){    }
       if (k != i) {    printf("\n");
         for(j=1; j <=ncovmodel; j++){    fprintf(ficlog,"\n");
          
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
           jk++;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
           fprintf(ficgp,"\n");    
         }    a=matrix(1,npar,1,npar);
       }    y=matrix(1,npar,1,npar);
     }    x=vector(1,npar);
     }    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
     for(jk=1; jk <=m; jk++) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    ludcmp(a,npar,indx,&pd);
    i=1;  
    for(k2=1; k2<=nlstate; k2++) {    for (j=1;j<=npar;j++) {
      k3=i;      for (i=1;i<=npar;i++) x[i]=0;
      for(k=1; k<=(nlstate+ndeath); k++) {      x[j]=1;
        if (k != k2){      lubksb(a,npar,indx,x);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      for (i=1;i<=npar;i++){ 
 ij=1;        matcov[i][j]=x[i];
         for(j=3; j <=ncovmodel; j++) {      }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    }
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;    printf("\n#Hessian matrix#\n");
           }    fprintf(ficlog,"\n#Hessian matrix#\n");
           else    for (i=1;i<=npar;i++) { 
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      for (j=1;j<=npar;j++) { 
         }        printf("%.3e ",hess[i][j]);
           fprintf(ficgp,")/(1");        fprintf(ficlog,"%.3e ",hess[i][j]);
              }
         for(k1=1; k1 <=nlstate; k1++){        printf("\n");
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      fprintf(ficlog,"\n");
 ij=1;    }
           for(j=3; j <=ncovmodel; j++){  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /* Recompute Inverse */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    for (i=1;i<=npar;i++)
             ij++;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
           }    ludcmp(a,npar,indx,&pd);
           else  
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /*  printf("\n#Hessian matrix recomputed#\n");
           }  
           fprintf(ficgp,")");    for (j=1;j<=npar;j++) {
         }      for (i=1;i<=npar;i++) x[i]=0;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      x[j]=1;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      lubksb(a,npar,indx,x);
         i=i+ncovmodel;      for (i=1;i<=npar;i++){ 
        }        y[i][j]=x[i];
      }        printf("%.3e ",y[i][j]);
    }        fprintf(ficlog,"%.3e ",y[i][j]);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      }
    }      printf("\n");
          fprintf(ficlog,"\n");
   fclose(ficgp);    }
 }  /* end gnuplot */    */
   
     free_matrix(a,1,npar,1,npar);
 /*************** Moving average **************/    free_matrix(y,1,npar,1,npar);
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
   int i, cpt, cptcod;    free_matrix(hess,1,npar,1,npar);
     for (agedeb=agemin; agedeb<=fage; agedeb++)  
       for (i=1; i<=nlstate;i++)  
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  }
           mobaverage[(int)agedeb][i][cptcod]=0.;  
      /*************** hessian matrix ****************/
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       for (i=1; i<=nlstate;i++){  {
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    int i;
           for (cpt=0;cpt<=4;cpt++){    int l=1, lmax=20;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    double k1,k2;
           }    double p2[MAXPARM+1]; /* identical to x */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    double res;
         }    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       }    double fx;
     }    int k=0,kmax=10;
        double l1;
 }  
     fx=func(x);
 /***********************************************/    for (i=1;i<=npar;i++) p2[i]=x[i];
 /**************** Main Program *****************/    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
 /***********************************************/      l1=pow(10,l);
       delts=delt;
 int main(int argc, char *argv[])      for(k=1 ; k <kmax; k=k+1){
 {        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
   double agedeb, agefin,hf;        p2[theta]=x[theta]-delt;
   double agemin=1.e20, agemax=-1.e20;        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
   double fret;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   double **xi,tmp,delta;        
   #ifdef DEBUGHESS
   double dum; /* Dummy variable */        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);
   double ***p3mat;        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);
   int *indx;  #endif
   char line[MAXLINE], linepar[MAXLINE];        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   char title[MAXLINE];        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          k=kmax;
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];        }
          else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];          k=kmax; l=lmax*10.;
         }
   char filerest[FILENAMELENGTH];        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   char fileregp[FILENAMELENGTH];          delts=delt;
   char popfile[FILENAMELENGTH];        }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      }
   int firstobs=1, lastobs=10;    }
   int sdeb, sfin; /* Status at beginning and end */    delti[theta]=delts;
   int c,  h , cpt,l;    return res; 
   int ju,jl, mi;    
   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;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   int hstepm, nhstepm;  {
   int *popage;/*boolprev=0 if date and zero if wave*/    int i;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
   double bage, fage, age, agelim, agebase;    double p2[MAXPARM+1];
   double ftolpl=FTOL;    int k;
   double **prlim;  
   double *severity;    fx=func(x);
   double ***param; /* Matrix of parameters */    for (k=1; k<=2; k++) {
   double  *p;      for (i=1;i<=npar;i++) p2[i]=x[i];
   double **matcov; /* Matrix of covariance */      p2[thetai]=x[thetai]+delti[thetai]/k;
   double ***delti3; /* Scale */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double *delti; /* Scale */      k1=func(p2)-fx;
   double ***eij, ***vareij;    
   double **varpl; /* Variances of prevalence limits by age */      p2[thetai]=x[thetai]+delti[thetai]/k;
   double *epj, vepp;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double kk1, kk2;      k2=func(p2)-fx;
   double *popeffectif,*popcount;    
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double yp,yp1,yp2;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";    
   char *alph[]={"a","a","b","c","d","e"}, str[4];      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
   char z[1]="c", occ;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 #include <sys/time.h>  #ifdef DEBUG
 #include <time.h>      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);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
    #endif
   /* long total_usecs;    }
   struct timeval start_time, end_time;    return res;
    }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  
   /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
   printf("\n%s",version);  { 
   if(argc <=1){    int i,imax,j,k; 
     printf("\nEnter the parameter file name: ");    double big,dum,sum,temp; 
     scanf("%s",pathtot);    double *vv; 
   }   
   else{    vv=vector(1,n); 
     strcpy(pathtot,argv[1]);    *d=1.0; 
   }    for (i=1;i<=n;i++) { 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      big=0.0; 
   /*cygwin_split_path(pathtot,path,optionfile);      for (j=1;j<=n;j++) 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        if ((temp=fabs(a[i][j])) > big) big=temp; 
   /* cutv(path,optionfile,pathtot,'\\');*/      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    } 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    for (j=1;j<=n;j++) { 
   chdir(path);      for (i=1;i<j;i++) { 
   replace(pathc,path);        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 /*-------- arguments in the command line --------*/        a[i][j]=sum; 
       } 
   strcpy(fileres,"r");      big=0.0; 
   strcat(fileres, optionfilefiname);      for (i=j;i<=n;i++) { 
   strcat(fileres,".txt");    /* Other files have txt extension */        sum=a[i][j]; 
         for (k=1;k<j;k++) 
   /*---------arguments file --------*/          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     printf("Problem with optionfile %s\n",optionfile);          big=dum; 
     goto end;          imax=i; 
   }        } 
       } 
   strcpy(filereso,"o");      if (j != imax) { 
   strcat(filereso,fileres);        for (k=1;k<=n;k++) { 
   if((ficparo=fopen(filereso,"w"))==NULL) {          dum=a[imax][k]; 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          a[imax][k]=a[j][k]; 
   }          a[j][k]=dum; 
         } 
   /* Reads comments: lines beginning with '#' */        *d = -(*d); 
   while((c=getc(ficpar))=='#' && c!= EOF){        vv[imax]=vv[j]; 
     ungetc(c,ficpar);      } 
     fgets(line, MAXLINE, ficpar);      indx[j]=imax; 
     puts(line);      if (a[j][j] == 0.0) a[j][j]=TINY; 
     fputs(line,ficparo);      if (j != n) { 
   }        dum=1.0/(a[j][j]); 
   ungetc(c,ficpar);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    } 
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    free_vector(vv,1,n);  /* Doesn't work */
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);  ;
 while((c=getc(ficpar))=='#' && c!= EOF){  } 
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  void lubksb(double **a, int n, int *indx, double b[]) 
     puts(line);  { 
     fputs(line,ficparo);    int i,ii=0,ip,j; 
   }    double sum; 
   ungetc(c,ficpar);   
      for (i=1;i<=n;i++) { 
          ip=indx[i]; 
   covar=matrix(0,NCOVMAX,1,n);      sum=b[ip]; 
   cptcovn=0;      b[ip]=b[i]; 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   ncovmodel=2+cptcovn;      else if (sum) ii=i; 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      b[i]=sum; 
      } 
   /* Read guess parameters */    for (i=n;i>=1;i--) { 
   /* Reads comments: lines beginning with '#' */      sum=b[i]; 
   while((c=getc(ficpar))=='#' && c!= EOF){      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     ungetc(c,ficpar);      b[i]=sum/a[i][i]; 
     fgets(line, MAXLINE, ficpar);    } 
     puts(line);  } 
     fputs(line,ficparo);  
   }  void pstamp(FILE *fichier)
   ungetc(c,ficpar);  {
      fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  }
     for(i=1; i <=nlstate; i++)  
     for(j=1; j <=nlstate+ndeath-1; j++){  /************ Frequencies ********************/
       fscanf(ficpar,"%1d%1d",&i1,&j1);  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[])
       fprintf(ficparo,"%1d%1d",i1,j1);  {  /* Some frequencies */
       printf("%1d%1d",i,j);    
       for(k=1; k<=ncovmodel;k++){    int i, m, jk, k1,i1, j1, bool, z1,j;
         fscanf(ficpar," %lf",&param[i][j][k]);    int first;
         printf(" %lf",param[i][j][k]);    double ***freq; /* Frequencies */
         fprintf(ficparo," %lf",param[i][j][k]);    double *pp, **prop;
       }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       fscanf(ficpar,"\n");    char fileresp[FILENAMELENGTH];
       printf("\n");    
       fprintf(ficparo,"\n");    pp=vector(1,nlstate);
     }    prop=matrix(1,nlstate,iagemin,iagemax+3);
      strcpy(fileresp,"p");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
   p=param[1][1];      printf("Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   /* Reads comments: lines beginning with '#' */      exit(0);
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     fgets(line, MAXLINE, ficpar);    j1=0;
     puts(line);    
     fputs(line,ficparo);    j=cptcoveff;
   }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   ungetc(c,ficpar);  
     first=1;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
   for(i=1; i <=nlstate; i++){    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
     for(j=1; j <=nlstate+ndeath-1; j++){    /*    j1++;
       fscanf(ficpar,"%1d%1d",&i1,&j1);  */
       printf("%1d%1d",i,j);    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
       fprintf(ficparo,"%1d%1d",i1,j1);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       for(k=1; k<=ncovmodel;k++){          scanf("%d", i);*/
         fscanf(ficpar,"%le",&delti3[i][j][k]);        for (i=-5; i<=nlstate+ndeath; i++)  
         printf(" %le",delti3[i][j][k]);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
         fprintf(ficparo," %le",delti3[i][j][k]);            for(m=iagemin; m <= iagemax+3; m++)
       }              freq[i][jk][m]=0;
       fscanf(ficpar,"\n");        
       printf("\n");        for (i=1; i<=nlstate; i++)  
       fprintf(ficparo,"\n");          for(m=iagemin; m <= iagemax+3; m++)
     }            prop[i][m]=0;
   }        
   delti=delti3[1][1];        dateintsum=0;
          k2cpt=0;
   /* Reads comments: lines beginning with '#' */        for (i=1; i<=imx; i++) {
   while((c=getc(ficpar))=='#' && c!= EOF){          bool=1;
     ungetc(c,ficpar);          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
     fgets(line, MAXLINE, ficpar);            for (z1=1; z1<=cptcoveff; z1++)       
     puts(line);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
     fputs(line,ficparo);                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
   }                bool=0;
   ungetc(c,ficpar);                /* 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],
   matcov=matrix(1,npar,1,npar);                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
   for(i=1; i <=npar; i++){                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
     fscanf(ficpar,"%s",&str);              } 
     printf("%s",str);          }
     fprintf(ficparo,"%s",str);   
     for(j=1; j <=i; j++){          if (bool==1){
       fscanf(ficpar," %le",&matcov[i][j]);            for(m=firstpass; m<=lastpass; m++){
       printf(" %.5le",matcov[i][j]);              k2=anint[m][i]+(mint[m][i]/12.);
       fprintf(ficparo," %.5le",matcov[i][j]);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fscanf(ficpar,"\n");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     printf("\n");                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     fprintf(ficparo,"\n");                if (m<lastpass) {
   }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   for(i=1; i <=npar; i++)                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     for(j=i+1;j<=npar;j++)                }
       matcov[i][j]=matcov[j][i];                
                    if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   printf("\n");                  dateintsum=dateintsum+k2;
                   k2cpt++;
                 }
     /*-------- data file ----------*/                /*}*/
     if((ficres =fopen(fileres,"w"))==NULL) {            }
       printf("Problem with resultfile: %s\n", fileres);goto end;          }
     }        } /* end i */
     fprintf(ficres,"#%s\n",version);         
            /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     if((fic=fopen(datafile,"r"))==NULL)    {        pstamp(ficresp);
       printf("Problem with datafile: %s\n", datafile);goto end;        if  (cptcovn>0) {
     }          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     n= lastobs;          fprintf(ficresp, "**********\n#");
     severity = vector(1,maxwav);          fprintf(ficlog, "\n#********** Variable "); 
     outcome=imatrix(1,maxwav+1,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     num=ivector(1,n);          fprintf(ficlog, "**********\n#");
     moisnais=vector(1,n);        }
     annais=vector(1,n);        for(i=1; i<=nlstate;i++) 
     moisdc=vector(1,n);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     andc=vector(1,n);        fprintf(ficresp, "\n");
     agedc=vector(1,n);        
     cod=ivector(1,n);        for(i=iagemin; i <= iagemax+3; i++){
     weight=vector(1,n);          if(i==iagemax+3){
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            fprintf(ficlog,"Total");
     mint=matrix(1,maxwav,1,n);          }else{
     anint=matrix(1,maxwav,1,n);            if(first==1){
     s=imatrix(1,maxwav+1,1,n);              first=0;
     adl=imatrix(1,maxwav+1,1,n);                  printf("See log file for details...\n");
     tab=ivector(1,NCOVMAX);            }
     ncodemax=ivector(1,8);            fprintf(ficlog,"Age %d", i);
           }
     i=1;          for(jk=1; jk <=nlstate ; jk++){
     while (fgets(line, MAXLINE, fic) != NULL)    {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       if ((i >= firstobs) && (i <=lastobs)) {              pp[jk] += freq[jk][m][i]; 
                  }
         for (j=maxwav;j>=1;j--){          for(jk=1; jk <=nlstate ; jk++){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            for(m=-1, pos=0; m <=0 ; m++)
           strcpy(line,stra);              pos += freq[jk][m][i];
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            if(pp[jk]>=1.e-10){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              if(first==1){
         }                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                      }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);            }else{
               if(first==1)
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          }
         for (j=ncov;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for(jk=1; jk <=nlstate ; jk++){
         }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         num[i]=atol(stra);              pp[jk] += freq[jk][m][i];
                  }       
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
           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;}*/            pos += pp[jk];
             posprop += prop[jk][i];
         i=i+1;          }
       }          for(jk=1; jk <=nlstate ; jk++){
     }            if(pos>=1.e-5){
     /* printf("ii=%d", ij);              if(first==1)
        scanf("%d",i);*/                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   imx=i-1; /* Number of individuals */              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
   /* for (i=1; i<=imx; i++){              if(first==1)
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;            }
     }            if( i <= iagemax){
               if(pos>=1.e-5){
     for (i=1; i<=imx; i++)                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/                /*probs[i][jk][j1]= pp[jk]/pos;*/
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   /* Calculation of the number of parameter from char model*/              }
   Tvar=ivector(1,15);              else
   Tprod=ivector(1,15);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   Tvaraff=ivector(1,15);            }
   Tvard=imatrix(1,15,1,2);          }
   Tage=ivector(1,15);                
              for(jk=-1; jk <=nlstate+ndeath; jk++)
   if (strlen(model) >1){            for(m=-1; m <=nlstate+ndeath; m++)
     j=0, j1=0, k1=1, k2=1;              if(freq[jk][m][i] !=0 ) {
     j=nbocc(model,'+');              if(first==1)
     j1=nbocc(model,'*');                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     cptcovn=j+1;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     cptcovprod=j1;              }
              if(i <= iagemax)
                fprintf(ficresp,"\n");
     strcpy(modelsav,model);          if(first==1)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            printf("Others in log...\n");
       printf("Error. Non available option model=%s ",model);          fprintf(ficlog,"\n");
       goto end;        }
     }        /*}*/
        }
     for(i=(j+1); i>=1;i--){    dateintmean=dateintsum/k2cpt; 
       cutv(stra,strb,modelsav,'+');   
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    fclose(ficresp);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
       /*scanf("%d",i);*/    free_vector(pp,1,nlstate);
       if (strchr(strb,'*')) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
         cutv(strd,strc,strb,'*');    /* End of Freq */
         if (strcmp(strc,"age")==0) {  }
           cptcovprod--;  
           cutv(strb,stre,strd,'V');  /************ Prevalence ********************/
           Tvar[i]=atoi(stre);  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)
           cptcovage++;  {  
             Tage[cptcovage]=i;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
             /*printf("stre=%s ", stre);*/       in each health status at the date of interview (if between dateprev1 and dateprev2).
         }       We still use firstpass and lastpass as another selection.
         else if (strcmp(strd,"age")==0) {    */
           cptcovprod--;   
           cutv(strb,stre,strc,'V');    int i, m, jk, k1, i1, j1, bool, z1,j;
           Tvar[i]=atoi(stre);    double ***freq; /* Frequencies */
           cptcovage++;    double *pp, **prop;
           Tage[cptcovage]=i;    double pos,posprop; 
         }    double  y2; /* in fractional years */
         else {    int iagemin, iagemax;
           cutv(strb,stre,strc,'V');    int first; /** to stop verbosity which is redirected to log file */
           Tvar[i]=ncov+k1;  
           cutv(strb,strc,strd,'V');    iagemin= (int) agemin;
           Tprod[k1]=i;    iagemax= (int) agemax;
           Tvard[k1][1]=atoi(strc);    /*pp=vector(1,nlstate);*/
           Tvard[k1][2]=atoi(stre);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
           Tvar[cptcovn+k2]=Tvard[k1][1];    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    j1=0;
           for (k=1; k<=lastobs;k++)    
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    /*j=cptcoveff;*/
           k1++;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           k2=k2+2;    
         }    first=1;
       }    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
       else {      /*for(i1=1; i1<=ncodemax[k1];i1++){
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        j1++;*/
        /*  scanf("%d",i);*/        
       cutv(strd,strc,strb,'V');        for (i=1; i<=nlstate; i++)  
       Tvar[i]=atoi(strc);          for(m=iagemin; m <= iagemax+3; m++)
       }            prop[i][m]=0.0;
       strcpy(modelsav,stra);         
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        for (i=1; i<=imx; i++) { /* Each individual */
         scanf("%d",i);*/          bool=1;
     }          if  (cptcovn>0) {
 }            for (z1=1; z1<=cptcoveff; z1++) 
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                bool=0;
   printf("cptcovprod=%d ", cptcovprod);          } 
   scanf("%d ",i);*/          if (bool==1) { 
     fclose(fic);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     /*  if(mle==1){*/              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     if (weightopt != 1) { /* Maximisation without weights*/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       for(i=1;i<=n;i++) weight[i]=1.0;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
     /*-calculation of age at interview from date of interview and age at death -*/                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     agev=matrix(1,maxwav,1,imx);                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
    for (i=1; i<=imx; i++)                  prop[s[m][i]][iagemax+3] += weight[i]; 
      for(m=2; (m<= maxwav); m++)                } 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){              }
          anint[m][i]=9999;            } /* end selection of waves */
          s[m][i]=-1;          }
        }        }
            for(i=iagemin; i <= iagemax+3; i++){  
     for (i=1; i<=imx; i++)  {          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);            posprop += prop[jk][i]; 
       for(m=1; (m<= maxwav); m++){          } 
         if(s[m][i] >0){          
           if (s[m][i] == nlstate+1) {          for(jk=1; jk <=nlstate ; jk++){     
             if(agedc[i]>0)            if( i <=  iagemax){ 
               if(moisdc[i]!=99 && andc[i]!=9999)              if(posprop>=1.e-5){ 
               agev[m][i]=agedc[i];                probs[i][jk][j1]= prop[jk][i]/posprop;
             else {              } else{
               if (andc[i]!=9999){                if(first==1){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                  first=0;
               agev[m][i]=-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]);
               }                }
             }              }
           }            } 
           else if(s[m][i] !=9){ /* Should no more exist */          }/* end jk */ 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        }/* end i */ 
             if(mint[m][i]==99 || anint[m][i]==9999)      /*} *//* end i1 */
               agev[m][i]=1;    } /* end j1 */
             else if(agev[m][i] <agemin){    
               agemin=agev[m][i];    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    /*free_vector(pp,1,nlstate);*/
             }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
             else if(agev[m][i] >agemax){  }  /* End of prevalence */
               agemax=agev[m][i];  
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  /************* Waves Concatenation ***************/
             }  
             /*agev[m][i]=anint[m][i]-annais[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)
             /*   agev[m][i] = age[i]+2*m;*/  {
           }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           else { /* =9 */       Death is a valid wave (if date is known).
             agev[m][i]=1;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
             s[m][i]=-1;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           }       and mw[mi+1][i]. dh depends on stepm.
         }       */
         else /*= 0 Unknown */  
           agev[m][i]=1;    int i, mi, m;
       }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           double sum=0., jmean=0.;*/
     }    int first;
     for (i=1; i<=imx; i++)  {    int j, k=0,jk, ju, jl;
       for(m=1; (m<= maxwav); m++){    double sum=0.;
         if (s[m][i] > (nlstate+ndeath)) {    first=0;
           printf("Error: Wrong value in nlstate or ndeath\n");      jmin=1e+5;
           goto end;    jmax=-1;
         }    jmean=0.;
       }    for(i=1; i<=imx; i++){
     }      mi=0;
       m=firstpass;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      while(s[m][i] <= nlstate){
         if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     free_vector(severity,1,maxwav);          mw[++mi][i]=m;
     free_imatrix(outcome,1,maxwav+1,1,n);        if(m >=lastpass)
     free_vector(moisnais,1,n);          break;
     free_vector(annais,1,n);        else
     /* free_matrix(mint,1,maxwav,1,n);          m++;
        free_matrix(anint,1,maxwav,1,n);*/      }/* end while */
     free_vector(moisdc,1,n);      if (s[m][i] > nlstate){
     free_vector(andc,1,n);        mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
               /* Only death is a correct wave */
     wav=ivector(1,imx);        mw[mi][i]=m;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
          wav[i]=mi;
     /* Concatenates waves */      if(mi==0){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        nbwarn++;
         if(first==0){
           printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       Tcode=ivector(1,100);          first=1;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        }
       ncodemax[1]=1;        if(first==1){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
              }
    codtab=imatrix(1,100,1,10);      } /* end mi==0 */
    h=0;    } /* End individuals */
    m=pow(2,cptcoveff);  
      for(i=1; i<=imx; i++){
    for(k=1;k<=cptcoveff; k++){      for(mi=1; mi<wav[i];mi++){
      for(i=1; i <=(m/pow(2,k));i++){        if (stepm <=0)
        for(j=1; j <= ncodemax[k]; j++){          dh[mi][i]=1;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        else{
            h++;          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
            if (h>m) h=1;codtab[h][k]=j;            if (agedc[i] < 2*AGESUP) {
          }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
        }              if(j==0) j=1;  /* Survives at least one month after exam */
      }              else if(j<0){
    }                nberr++;
                 printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 j=1; /* Temporary Dangerous patch */
    /*for(i=1; i <=m ;i++){                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);
      for(k=1; k <=cptcovn; k++){                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]);
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);                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);
      }              }
      printf("\n");              k=k+1;
    }              if (j >= jmax){
    scanf("%d",i);*/                jmax=j;
                    ijmax=i;
    /* Calculates basic frequencies. Computes observed prevalence at single age              }
        and prints on file fileres'p'. */              if (j <= jmin){
                 jmin=j;
                    ijmin=i;
                  }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              sum=sum+j;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            }
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          }
                else{
     /* For Powell, parameters are in a vector p[] starting at p[1]            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
             k=k+1;
     if(mle==1){            if (j >= jmax) {
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              jmax=j;
     }              ijmax=i;
                }
     /*--------- results files --------------*/            else if (j <= jmin){
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);              jmin=j;
                ijmin=i;
             }
    jk=1;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
    fprintf(ficres,"# Parameters\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]);*/
    printf("# Parameters\n");            if(j<0){
    for(i=1,jk=1; i <=nlstate; i++){              nberr++;
      for(k=1; k <=(nlstate+ndeath); k++){              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]);
        if (k != i)              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
          {            }
            printf("%d%d ",i,k);            sum=sum+j;
            fprintf(ficres,"%1d%1d ",i,k);          }
            for(j=1; j <=ncovmodel; j++){          jk= j/stepm;
              printf("%f ",p[jk]);          jl= j -jk*stepm;
              fprintf(ficres,"%f ",p[jk]);          ju= j -(jk+1)*stepm;
              jk++;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
            }            if(jl==0){
            printf("\n");              dh[mi][i]=jk;
            fprintf(ficres,"\n");              bh[mi][i]=0;
          }            }else{ /* We want a negative bias in order to only have interpolation ie
      }                    * to avoid the price of an extra matrix product in likelihood */
    }              dh[mi][i]=jk+1;
  if(mle==1){              bh[mi][i]=ju;
     /* Computing hessian and covariance matrix */            }
     ftolhess=ftol; /* Usually correct */          }else{
     hesscov(matcov, p, npar, delti, ftolhess, func);            if(jl <= -ju){
  }              dh[mi][i]=jk;
     fprintf(ficres,"# Scales\n");              bh[mi][i]=jl;       /* bias is positive if real duration
     printf("# Scales\n");                                   * is higher than the multiple of stepm and negative otherwise.
      for(i=1,jk=1; i <=nlstate; i++){                                   */
       for(j=1; j <=nlstate+ndeath; j++){            }
         if (j!=i) {            else{
           fprintf(ficres,"%1d%1d",i,j);              dh[mi][i]=jk+1;
           printf("%1d%1d",i,j);              bh[mi][i]=ju;
           for(k=1; k<=ncovmodel;k++){            }
             printf(" %.5e",delti[jk]);            if(dh[mi][i]==0){
             fprintf(ficres," %.5e",delti[jk]);              dh[mi][i]=1; /* At least one step */
             jk++;              bh[mi][i]=ju; /* At least one step */
           }              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
           printf("\n");            }
           fprintf(ficres,"\n");          } /* end if mle */
         }        }
       }      } /* end wave */
      }    }
        jmean=sum/k;
     k=1;    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
     fprintf(ficres,"# Covariance\n");    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
     printf("# Covariance\n");   }
     for(i=1;i<=npar;i++){  
       /*  if (k>nlstate) k=1;  /*********** Tricode ****************************/
       i1=(i-1)/(ncovmodel*nlstate)+1;  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  {
       printf("%s%d%d",alph[k],i1,tab[i]);*/    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
       fprintf(ficres,"%3d",i);    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
       printf("%3d",i);    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
       for(j=1; j<=i;j++){     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
         fprintf(ficres," %.5e",matcov[i][j]);    /* nbcode[Tvar[j]][1]= 
         printf(" %.5e",matcov[i][j]);    */
       }  
       fprintf(ficres,"\n");    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
       printf("\n");    int modmaxcovj=0; /* Modality max of covariates j */
       k++;    int cptcode=0; /* Modality max of covariates j */
     }    int modmincovj=0; /* Modality min of covariates j */
      
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);    cptcoveff=0; 
       fgets(line, MAXLINE, ficpar);   
       puts(line);    for (k=-1; k < maxncov; k++) Ndum[k]=0;
       fputs(line,ficparo);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
     }  
     ungetc(c,ficpar);    /* Loop on covariates without age and products */
      for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
                                     modality of this covariate Vj*/ 
     if (fage <= 2) {        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
       bage = agemin;                                      * If product of Vn*Vm, still boolean *:
       fage = agemax;                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
     }                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
            /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                                        modality of the nth covariate of individual i. */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        if (ij > modmaxcovj)
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          modmaxcovj=ij; 
          else if (ij < modmincovj) 
     while((c=getc(ficpar))=='#' && c!= EOF){          modmincovj=ij; 
     ungetc(c,ficpar);        if ((ij < -1) && (ij > NCOVMAX)){
     fgets(line, MAXLINE, ficpar);          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
     puts(line);          exit(1);
     fputs(line,ficparo);        }else
   }        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
   ungetc(c,ficpar);        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
          /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        /* getting the maximum value of the modality of the covariate
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);           female is 1, then modmaxcovj=1.*/
            }
   while((c=getc(ficpar))=='#' && c!= EOF){      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
     ungetc(c,ficpar);      cptcode=modmaxcovj;
     fgets(line, MAXLINE, ficpar);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
     puts(line);     /*for (i=0; i<=cptcode; i++) {*/
     fputs(line,ficparo);      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
   }        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
   ungetc(c,ficpar);        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
            ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
         }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
    dateprev2=anprev2+mprev2/12.+jprev2/365.;           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
       } /* Ndum[-1] number of undefined modalities */
   fscanf(ficpar,"pop_based=%d\n",&popbased);  
    fprintf(ficparo,"pop_based=%d\n",popbased);        /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
    fprintf(ficres,"pop_based=%d\n",popbased);        /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
       /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
   while((c=getc(ficpar))=='#' && c!= EOF){         modmincovj=3; modmaxcovj = 7;
     ungetc(c,ficpar);         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
     fgets(line, MAXLINE, ficpar);         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
     puts(line);         variables V1_1 and V1_2.
     fputs(line,ficparo);         nbcode[Tvar[j]][ij]=k;
   }         nbcode[Tvar[j]][1]=0;
   ungetc(c,ficpar);         nbcode[Tvar[j]][2]=1;
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mob_average=%d\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);         nbcode[Tvar[j]][3]=2;
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mob_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      */
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mob_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      ij=1; /* ij is similar to i but can jumps over null modalities */
       for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
           /*recode from 0 */
 /*------------ gnuplot -------------*/          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemax,fage, pathc,p);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                                         k is a modality. If we have model=V1+V1*sex 
 /*------------ free_vector  -------------*/                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
  chdir(path);            ij++;
            }
  free_ivector(wav,1,imx);          if (ij > ncodemax[j]) break; 
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        }  /* end of loop on */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        } /* end of loop on modality */ 
  free_ivector(num,1,n);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
  free_vector(agedc,1,n);    
  /*free_matrix(covar,1,NCOVMAX,1,n);*/   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
  fclose(ficparo);    
  fclose(ficres);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
       /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
   /* Reads comments: lines beginning with '#' */     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
   while((c=getc(ficpar))=='#' && c!= EOF){     Ndum[ij]++; 
     ungetc(c,ficpar);   } 
     fgets(line, MAXLINE, ficpar);  
     puts(line);   ij=1;
     fputs(line,ficparo);   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   }     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   ungetc(c,ficpar);     if((Ndum[i]!=0) && (i<=ncovcol)){
         /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);       Tvaraff[ij]=i; /*For printing (unclear) */
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);       ij++;
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);     }else
 /*--------- index.htm --------*/         Tvaraff[ij]=0;
    }
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);   ij--;
    cptcoveff=ij; /*Number of total covariates*/
    
   /*--------------- Prevalence limit --------------*/  }
    
   strcpy(filerespl,"pl");  
   strcat(filerespl,fileres);  /*********** Health Expectancies ****************/
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  {
   fprintf(ficrespl,"#Prevalence limit\n");    /* Health expectancies, no variances */
   fprintf(ficrespl,"#Age ");    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    int nhstepma, nstepma; /* Decreasing with age */
   fprintf(ficrespl,"\n");    double age, agelim, hf;
      double ***p3mat;
   prlim=matrix(1,nlstate,1,nlstate);    double eip;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pstamp(ficreseij);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficreseij,"# Age");
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    for(i=1; i<=nlstate;i++){
   k=0;      for(j=1; j<=nlstate;j++){
   agebase=agemin;        fprintf(ficreseij," e%1d%1d ",i,j);
   agelim=agemax;      }
   ftolpl=1.e-10;      fprintf(ficreseij," e%1d. ",i);
   i1=cptcoveff;    }
   if (cptcovn < 1){i1=1;}    fprintf(ficreseij,"\n");
   
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if(estepm < stepm){
         k=k+1;      printf ("Problem %d lower than %d\n",estepm, stepm);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    }
         fprintf(ficrespl,"\n#******");    else  hstepm=estepm;   
         for(j=1;j<=cptcoveff;j++)    /* We compute the life expectancy from trapezoids spaced every estepm months
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     * This is mainly to measure the difference between two models: for example
         fprintf(ficrespl,"******\n");     * 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 
         for (age=agebase; age<=agelim; age++){     * progression in between and thus overestimating or underestimating according
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);     * to the curvature of the survival function. If, for the same date, we 
           fprintf(ficrespl,"%.0f",age );     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           for(i=1; i<=nlstate;i++)     * to compare the new estimate of Life expectancy with the same linear 
           fprintf(ficrespl," %.5f", prlim[i][i]);     * hypothesis. A more precise result, taking into account a more precise
           fprintf(ficrespl,"\n");     * curvature will be obtained if estepm is as small as stepm. */
         }  
       }    /* For example we decided to compute the life expectancy with the smallest unit */
     }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   fclose(ficrespl);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   /*------------- h Pij x at various ages ------------*/       Look at hpijx to understand the reason of that which relies in memory size
         and note for a fixed period like estepm months */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   if((ficrespij=fopen(filerespij,"w"))==NULL) {       survival function given by stepm (the optimization length). Unfortunately it
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;       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 
   printf("Computing pij: result on file '%s' \n", filerespij);       results. So we changed our mind and took the option of the best precision.
      */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   /*if (stepm<=24) stepsize=2;*/  
     agelim=AGESUP;
   agelim=AGESUP;    /* If stepm=6 months */
   hstepm=stepsize*YEARM; /* Every year of age */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
        
   k=0;  /* nhstepm age range expressed in number of stepm */
   for(cptcov=1;cptcov<=i1;cptcov++){    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       k=k+1;    /* if (stepm >= YEARM) hstepm=1;*/
         fprintf(ficrespij,"\n#****** ");    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         for(j=1;j<=cptcoveff;j++)    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");    for (age=bage; age<=fage; age ++){ 
              nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      /* if (stepm >= YEARM) hstepm=1;*/
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;      /* If stepm=6 months */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        /* Computed by stepm unit matrices, product of hstepma matrices, stored
           fprintf(ficrespij,"# Age");         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           for(i=1; i<=nlstate;i++)      
             for(j=1; j<=nlstate+ndeath;j++)      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
               fprintf(ficrespij," %1d-%1d",i,j);      
           fprintf(ficrespij,"\n");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           for (h=0; h<=nhstepm; h++){      
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      printf("%d|",(int)age);fflush(stdout);
             for(i=1; i<=nlstate;i++)      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
               for(j=1; j<=nlstate+ndeath;j++)      
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      /* Computing expectancies */
             fprintf(ficrespij,"\n");      for(i=1; i<=nlstate;i++)
           }        for(j=1; j<=nlstate;j++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           fprintf(ficrespij,"\n");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
         }            
     }            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   }  
           }
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  
       fprintf(ficreseij,"%3.0f",age );
   fclose(ficrespij);      for(i=1; i<=nlstate;i++){
         eip=0;
   if(stepm == 1) {        for(j=1; j<=nlstate;j++){
   /*---------- Forecasting ------------------*/          eip +=eij[i][j][(int)age];
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
   /*printf("calage= %f", calagedate);*/        fprintf(ficreseij,"%9.4f", eip );
        }
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      fprintf(ficreseij,"\n");
       
     }
   strcpy(fileresf,"f");    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcat(fileresf,fileres);    printf("\n");
   if((ficresf=fopen(fileresf,"w"))==NULL) {    fprintf(ficlog,"\n");
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    
   }  }
   printf("Computing forecasting: result on file '%s' \n", fileresf);  
   void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   free_matrix(mint,1,maxwav,1,n);  
   free_matrix(anint,1,maxwav,1,n);  {
   free_matrix(agev,1,maxwav,1,imx);    /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
   /* Mobile average */    */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
   if (mobilav==1) {    double ***p3matp, ***p3matm, ***varhe;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double **dnewm,**doldm;
     movingaverage(agedeb, fage, agemin, mobaverage);    double *xp, *xm;
   }    double **gp, **gm;
     double ***gradg, ***trgradg;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int theta;
   if (stepm<=12) stepsize=1;  
     double eip, vip;
   agelim=AGESUP;  
   /*hstepm=stepsize*YEARM; *//* Every year of age */    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   hstepm=1;    xp=vector(1,npar);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */    xm=vector(1,npar);
   yp1=modf(dateintmean,&yp);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   anprojmean=yp;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   yp2=modf((yp1*12),&yp);    
   mprojmean=yp;    pstamp(ficresstdeij);
   yp1=modf((yp2*30.5),&yp);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   jprojmean=yp;    fprintf(ficresstdeij,"# Age");
   if(jprojmean==0) jprojmean=1;    for(i=1; i<=nlstate;i++){
   if(mprojmean==0) jprojmean=1;      for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      fprintf(ficresstdeij," e%1d. ",i);
     }
   if (popforecast==1) {    fprintf(ficresstdeij,"\n");
     if((ficpop=fopen(popfile,"r"))==NULL)    {  
       printf("Problem with population file : %s\n",popfile);goto end;    pstamp(ficrescveij);
     }    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     popage=ivector(0,AGESUP);    fprintf(ficrescveij,"# Age");
     popeffectif=vector(0,AGESUP);    for(i=1; i<=nlstate;i++)
     popcount=vector(0,AGESUP);      for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
     i=1;          for(i2=1; i2<=nlstate;i2++)
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)          for(j2=1; j2<=nlstate;j2++){
       {            cptj2= (j2-1)*nlstate+i2;
         i=i+1;            if(cptj2 <= cptj)
       }              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     imx=i;          }
          }
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    fprintf(ficrescveij,"\n");
   }    
     if(estepm < stepm){
   for(cptcov=1;cptcov<=i1;cptcov++){      printf ("Problem %d lower than %d\n",estepm, stepm);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    }
       k=k+1;    else  hstepm=estepm;   
       fprintf(ficresf,"\n#******");    /* We compute the life expectancy from trapezoids spaced every estepm months
       for(j=1;j<=cptcoveff;j++) {     * This is mainly to measure the difference between two models: for example
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     * 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 
       fprintf(ficresf,"******\n");     * progression in between and thus overestimating or underestimating according
       fprintf(ficresf,"# StartingAge FinalAge");     * to the curvature of the survival function. If, for the same date, we 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       if (popforecast==1)  fprintf(ficresf," [Population]");     * to compare the new estimate of Life expectancy with the same linear 
           * hypothesis. A more precise result, taking into account a more precise
      for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {     * curvature will be obtained if estepm is as small as stepm. */
         fprintf(ficresf,"\n");  
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){       nhstepm is the number of hstepm from age to agelim 
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       nstepm is the number of stepm from age to agelin. 
         nhstepm = nhstepm/hstepm;       Look at hpijx to understand the reason of that which relies in memory size
               and note for a fixed period like estepm months */
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         oldm=oldms;savm=savms;       survival function given by stepm (the optimization length). Unfortunately it
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         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 
         for (h=0; h<=nhstepm; h++){       results. So we changed our mind and took the option of the best precision.
           if (h==(int) (calagedate+YEARM*cpt)) {    */
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           }  
           for(j=1; j<=nlstate+ndeath;j++) {    /* If stepm=6 months */
             kk1=0.;kk2=0;    /* nhstepm age range expressed in number of stepm */
             for(i=1; i<=nlstate;i++) {            agelim=AGESUP;
               if (mobilav==1)    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
               else {    /* if (stepm >= YEARM) hstepm=1;*/
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                    
               }    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
             }    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
              gp=matrix(0,nhstepm,1,nlstate*nlstate);
             if (h==(int)(calagedate+12*cpt)){    gm=matrix(0,nhstepm,1,nlstate*nlstate);
               fprintf(ficresf," %.3f", kk1);  
                  for (age=bage; age<=fage; age ++){ 
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
             }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           }      /* if (stepm >= YEARM) hstepm=1;*/
         }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }      /* If stepm=6 months */
      }      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     }         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   }      
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
   if (popforecast==1) {      /* Computing  Variances of health expectancies */
     free_ivector(popage,0,AGESUP);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     free_vector(popeffectif,0,AGESUP);         decrease memory allocation */
     free_vector(popcount,0,AGESUP);      for(theta=1; theta <=npar; theta++){
   }        for(i=1; i<=npar; i++){ 
   free_imatrix(s,1,maxwav+1,1,n);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   free_vector(weight,1,n);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
   fclose(ficresf);        }
   }/* End forecasting */        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
   else{        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     erreur=108;    
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
   }            for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
                gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
   /*---------- Health expectancies and variances ------------*/            }
           }
   strcpy(filerest,"t");        }
   strcat(filerest,fileres);       
   if((ficrest=fopen(filerest,"w"))==NULL) {        for(ij=1; ij<= nlstate*nlstate; ij++)
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          for(h=0; h<=nhstepm-1; h++){
   }            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          }
       }/* End theta */
       
   strcpy(filerese,"e");      
   strcat(filerese,fileres);      for(h=0; h<=nhstepm-1; h++)
   if((ficreseij=fopen(filerese,"w"))==NULL) {        for(j=1; j<=nlstate*nlstate;j++)
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          for(theta=1; theta <=npar; theta++)
   }            trgradg[h][j][theta]=gradg[h][theta][j];
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      
   
  strcpy(fileresv,"v");       for(ij=1;ij<=nlstate*nlstate;ij++)
   strcat(fileresv,fileres);        for(ji=1;ji<=nlstate*nlstate;ji++)
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          varhe[ij][ji][(int)age] =0.;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }       printf("%d|",(int)age);fflush(stdout);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
   k=0;        for(k=0;k<=nhstepm-1;k++){
   for(cptcov=1;cptcov<=i1;cptcov++){          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       k=k+1;          for(ij=1;ij<=nlstate*nlstate;ij++)
       fprintf(ficrest,"\n#****** ");            for(ji=1;ji<=nlstate*nlstate;ji++)
       for(j=1;j<=cptcoveff;j++)              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }
       fprintf(ficrest,"******\n");      }
   
       fprintf(ficreseij,"\n#****** ");      /* Computing expectancies */
       for(j=1;j<=cptcoveff;j++)      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      for(i=1; i<=nlstate;i++)
       fprintf(ficreseij,"******\n");        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       fprintf(ficresvij,"\n#****** ");            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
       for(j=1;j<=cptcoveff;j++)            
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       fprintf(ficresvij,"******\n");  
           }
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;      fprintf(ficresstdeij,"%3.0f",age );
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        for(i=1; i<=nlstate;i++){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        eip=0.;
       oldm=oldms;savm=savms;        vip=0.;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        for(j=1; j<=nlstate;j++){
                eip += eij[i][j][(int)age];
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
       fprintf(ficrest,"\n");          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
                }
       hf=1;        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       if (stepm >= YEARM) hf=stepm/YEARM;      }
       epj=vector(1,nlstate+1);      fprintf(ficresstdeij,"\n");
       for(age=bage; age <=fage ;age++){  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      fprintf(ficrescveij,"%3.0f",age );
         if (popbased==1) {      for(i=1; i<=nlstate;i++)
           for(i=1; i<=nlstate;i++)        for(j=1; j<=nlstate;j++){
             prlim[i][i]=probs[(int)age][i][k];          cptj= (j-1)*nlstate+i;
         }          for(i2=1; i2<=nlstate;i2++)
                    for(j2=1; j2<=nlstate;j2++){
         fprintf(ficrest," %.0f",age);              cptj2= (j2-1)*nlstate+i2;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){              if(cptj2 <= cptj)
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];            }
           }        }
           epj[nlstate+1] +=epj[j];      fprintf(ficrescveij,"\n");
         }     
         for(i=1, vepp=0.;i <=nlstate;i++)    }
           for(j=1;j <=nlstate;j++)    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
             vepp += vareij[i][j][(int)age];    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
         for(j=1;j <=nlstate;j++){    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrest,"\n");    printf("\n");
       }    fprintf(ficlog,"\n");
     }  
   }    free_vector(xm,1,npar);
            free_vector(xp,1,npar);
            free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
  fclose(ficreseij);  }
  fclose(ficresvij);  
   fclose(ficrest);  /************ Variance ******************/
   fclose(ficpar);  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   free_vector(epj,1,nlstate+1);  {
   /*  scanf("%d ",i); */    /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   /*------- Variance limit prevalence------*/      /* double **newm;*/
     double **dnewm,**doldm;
 strcpy(fileresvpl,"vpl");    double **dnewmp,**doldmp;
   strcat(fileresvpl,fileres);    int i, j, nhstepm, hstepm, h, nstepm ;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    int k, cptcode;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    double *xp;
     exit(0);    double **gp, **gm;  /* for var eij */
   }    double ***gradg, ***trgradg; /*for var eij */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
  k=0;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
  for(cptcov=1;cptcov<=i1;cptcov++){    double ***p3mat;
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double age,agelim, hf;
      k=k+1;    double ***mobaverage;
      fprintf(ficresvpl,"\n#****** ");    int theta;
      for(j=1;j<=cptcoveff;j++)    char digit[4];
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    char digitp[25];
      fprintf(ficresvpl,"******\n");  
          char fileresprobmorprev[FILENAMELENGTH];
      varpl=matrix(1,nlstate,(int) bage, (int) fage);  
      oldm=oldms;savm=savms;    if(popbased==1){
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      if(mobilav!=0)
    }        strcpy(digitp,"-populbased-mobilav-");
  }      else strcpy(digitp,"-populbased-nomobil-");
     }
   fclose(ficresvpl);    else 
       strcpy(digitp,"-stablbased-");
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    if (mobilav!=0) {
        mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
          printf(" Error in movingaverage mobilav=%d\n",mobilav);
        }
   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);    strcpy(fileresprobmorprev,"prmorprev"); 
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    sprintf(digit,"%-d",ij);
      /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   free_matrix(matcov,1,npar,1,npar);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   free_vector(delti,1,npar);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
      strcat(fileresprobmorprev,fileres);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
   if(erreur >0)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     printf("End of Imach with error %d\n",erreur);    }
   else   printf("End of Imach\n");    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */   
      fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   /* 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);*/    pstamp(ficresprobmorprev);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    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);
   /*------ End -----------*/    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
  end:      for(i=1; i<=nlstate;i++)
 #ifdef windows        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   /* chdir(pathcd);*/    }  
 #endif    fprintf(ficresprobmorprev,"\n");
  /*system("wgnuplot graph.plt");*/    fprintf(ficgp,"\n# Routine varevsij");
  /*system("../gp37mgw/wgnuplot graph.plt");*/    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
  /*system("cd ../gp37mgw");*/    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");
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
  strcpy(plotcmd,GNUPLOTPROGRAM);  /*   } */
  strcat(plotcmd," ");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
  strcat(plotcmd,optionfilegnuplot);    pstamp(ficresvij);
  system(plotcmd);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
 #ifdef windows      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);
   while (z[0] != 'q') {    else
     chdir(path);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    fprintf(ficresvij,"# Age");
     scanf("%s",z);    for(i=1; i<=nlstate;i++)
     if (z[0] == 'c') system("./imach");      for(j=1; j<=nlstate;j++)
     else if (z[0] == 'e') {        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
       chdir(path);    fprintf(ficresvij,"\n");
       system(optionfilehtm);  
     }    xp=vector(1,npar);
     else if (z[0] == 'q') exit(0);    dnewm=matrix(1,nlstate,1,npar);
   }    doldm=matrix(1,nlstate,1,nlstate);
 #endif    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
 }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **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 */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_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.tv_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';
      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.tv_sec-start_time.tv_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);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     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(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  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");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error 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(" Successul, 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 OSX
         sprintf(pplotcmd, "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.1.25  
changed lines
  Added in v.1.154


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