Diff for /imach/src/imach.c between versions 1.41 and 1.163

version 1.41, 2002/05/07 15:53:01 version 1.163, 2014/12/16 10:30:11
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.163  2014/12/16 10:30:11  brouard
      * imach.c (Module): Merging 1.61 to 1.162
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.162  2014/09/25 11:43:39  brouard
   first survey ("cross") where individuals from different ages are    Summary: temporary backup 0.99!
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.1  2014/09/16 11:06:58  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: With some code (wrong) for nlopt
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Author:
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.161  2014/09/15 20:41:41  brouard
   simplest model is the multinomial logistic model where pij is the    Summary: Problem with macro SQR on Intel compiler
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.160  2014/09/02 09:24:05  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    *** empty log message ***
   '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 1.159  2014/09/01 10:34:10  brouard
   where the markup *Covariates have to be included here again* invites    Summary: WIN32
   you to do it.  More covariates you add, slower the    Author: Brouard
   convergence.  
     Revision 1.158  2014/08/27 17:11:51  brouard
   The advantage of this computer programme, compared to a simple    *** empty log message ***
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.157  2014/08/27 16:26:55  brouard
   intermediate interview, the information is lost, but taken into    Summary: Preparing windows Visual studio version
   account using an interpolation or extrapolation.      Author: Brouard
   
   hPijx is the probability to be observed in state i at age x+h    In order to compile on Visual studio, time.h is now correct and time_t
   conditional to the observed state i at age x. The delay 'h' can be    and tm struct should be used. difftime should be used but sometimes I
   split into an exact number (nh*stepm) of unobserved intermediate    just make the differences in raw time format (time(&now).
   states. This elementary transition (by month or quarter trimester,    Trying to suppress #ifdef LINUX
   semester or year) is model as a multinomial logistic.  The hPx    Add xdg-open for __linux in order to open default browser.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.156  2014/08/25 20:10:10  brouard
   hPijx.    *** empty log message ***
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.155  2014/08/25 18:32:34  brouard
   of the life expectancies. It also computes the prevalence limits.    Summary: New compile, minor changes
      Author: Brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.154  2014/06/20 17:32:08  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: Outputs now all graphs of convergence to period prevalence
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.153  2014/06/20 16:45:46  brouard
   software can be distributed freely for non commercial use. Latest version    Summary: If 3 live state, convergence to period prevalence on same graph
   can be accessed at http://euroreves.ined.fr/imach .    Author: Brouard
   **********************************************************************/  
      Revision 1.152  2014/06/18 17:54:09  brouard
 #include <math.h>    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.151  2014/06/18 16:43:30  brouard
 #include <unistd.h>    *** empty log message ***
   
 #define MAXLINE 256    Revision 1.150  2014/06/18 16:42:35  brouard
 #define GNUPLOTPROGRAM "wgnuplot"    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Author: brouard
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.149  2014/06/18 15:51:14  brouard
 #define windows    Summary: Some fixes in parameter files errors
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Author: Nicolas Brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.148  2014/06/17 17:38:48  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Summary: Nothing new
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Author: Brouard
   
 #define NINTERVMAX 8    Just a new packaging for OS/X version 0.98nS
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.147  2014/06/16 10:33:11  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    *** empty log message ***
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.146  2014/06/16 10:20:28  brouard
 #define AGESUP 130    Summary: Merge
 #define AGEBASE 40    Author: Brouard
   
     Merge, before building revised version.
 int erreur; /* Error number */  
 int nvar;    Revision 1.145  2014/06/10 21:23:15  brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Summary: Debugging with valgrind
 int npar=NPARMAX;    Author: Nicolas Brouard
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Lot of changes in order to output the results with some covariates
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    After the Edimburgh REVES conference 2014, it seems mandatory to
 int popbased=0;    improve the code.
     No more memory valgrind error but a lot has to be done in order to
 int *wav; /* Number of waves for this individuual 0 is possible */    continue the work of splitting the code into subroutines.
 int maxwav; /* Maxim number of waves */    Also, decodemodel has been improved. Tricode is still not
 int jmin, jmax; /* min, max spacing between 2 waves */    optimal. nbcode should be improved. Documentation has been added in
 int mle, weightopt;    the source 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 1.143  2014/01/26 09:45:38  brouard
 double jmean; /* Mean space between 2 waves */    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 FILE *ficgp,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.142  2014/01/26 03:57:36  brouard
   char filerese[FILENAMELENGTH];    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    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 NR_END 1  
 #define FREE_ARG char*    Revision 1.140  2011/09/02 10:37:54  brouard
 #define FTOL 1.0e-10    Summary: times.h is ok with mingw32 now.
   
 #define NRANSI    Revision 1.139  2010/06/14 07:50:17  brouard
 #define ITMAX 200    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
     I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 #define TOL 2.0e-4  
     Revision 1.138  2010/04/30 18:19:40  brouard
 #define CGOLD 0.3819660    *** empty log message ***
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.137  2010/04/29 18:11:38  brouard
     (Module): Checking covariates for more complex models
 #define GOLD 1.618034    than V1+V2. A lot of change to be done. Unstable.
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.136  2010/04/26 20:30:53  brouard
     (Module): merging some libgsl code. Fixing computation
 static double maxarg1,maxarg2;    of likelione (using inter/intrapolation if mle = 0) in order to
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    get same likelihood as if mle=1.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Some cleaning of code and comments added.
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.135  2009/10/29 15:33:14  brouard
 #define rint(a) floor(a+0.5)    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
 static double sqrarg;    Revision 1.134  2009/10/29 13:18:53  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.133  2009/07/06 10:21:25  brouard
 int imx;    just nforces
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.132  2009/07/06 08:22:05  brouard
     Many tings
 int estepm;  
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Revision 1.131  2009/06/20 16:22:47  brouard
     Some dimensions resccaled
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.130  2009/05/26 06:44:34  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (Module): Max Covariate is now set to 20 instead of 8. A
 double **pmmij, ***probs, ***mobaverage;    lot of cleaning with variables initialized to 0. Trying to make
 double dateintmean=0;    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
 double *weight;    Revision 1.129  2007/08/31 13:49:27  lievre
 int **s; /* Status */    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.128  2006/06/30 13:02:05  brouard
     (Module): Clarifications on computing e.j
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 /**************** split *************************/    imach-114 because nhstepm was no more computed in the age
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    loop. Now we define nhstepma in the age loop.
 {    (Module): In order to speed up (in case of numerous covariates) we
    char *s;                             /* pointer */    compute health expectancies (without variances) in a first step
    int  l1, l2;                         /* length counters */    and then all the health expectancies with variances or standard
     deviation (needs data from the Hessian matrices) which slows the
    l1 = strlen( path );                 /* length of path */    computation.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    In the future we should be able to stop the program is only health
 #ifdef windows    expectancies and graph are needed without standard deviations.
    s = strrchr( path, '\\' );           /* find last / */  
 #else    Revision 1.126  2006/04/28 17:23:28  brouard
    s = strrchr( path, '/' );            /* find last / */    (Module): Yes the sum of survivors was wrong since
 #endif    imach-114 because nhstepm was no more computed in the age
    if ( s == NULL ) {                   /* no directory, so use current */    loop. Now we define nhstepma in the age loop.
 #if     defined(__bsd__)                /* get current working directory */    Version 0.98h
       extern char       *getwd( );  
     Revision 1.125  2006/04/04 15:20:31  lievre
       if ( getwd( dirc ) == NULL ) {    Errors in calculation of health expectancies. Age was not initialized.
 #else    Forecasting file added.
       extern char       *getcwd( );  
     Revision 1.124  2006/03/22 17:13:53  lievre
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Parameters are printed with %lf instead of %f (more numbers after the comma).
 #endif    The log-likelihood is printed in the log file
          return( GLOCK_ERROR_GETCWD );  
       }    Revision 1.123  2006/03/20 10:52:43  brouard
       strcpy( name, path );             /* we've got it */    * imach.c (Module): <title> changed, corresponds to .htm file
    } else {                             /* strip direcotry from path */    name. <head> headers where missing.
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    * imach.c (Module): Weights can have a decimal point as for
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    English (a comma might work with a correct LC_NUMERIC environment,
       strcpy( name, s );                /* save file name */    otherwise the weight is truncated).
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Modification of warning when the covariates values are not 0 or
       dirc[l1-l2] = 0;                  /* add zero */    1.
    }    Version 0.98g
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    Revision 1.122  2006/03/20 09:45:41  brouard
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    (Module): Weights can have a decimal point as for
 #else    English (a comma might work with a correct LC_NUMERIC environment,
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    otherwise the weight is truncated).
 #endif    Modification of warning when the covariates values are not 0 or
    s = strrchr( name, '.' );            /* find last / */    1.
    s++;    Version 0.98g
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Revision 1.121  2006/03/16 17:45:01  lievre
    l2= strlen( s)+1;    * imach.c (Module): Comments concerning covariates added
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    * imach.c (Module): refinements in the computation of lli if
    return( 0 );                         /* we're done */    status=-2 in order to have more reliable computation if stepm is
 }    not 1 month. Version 0.98f
   
     Revision 1.120  2006/03/16 15:10:38  lievre
 /******************************************/    (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 void replace(char *s, char*t)    not 1 month. Version 0.98f
 {  
   int i;    Revision 1.119  2006/03/15 17:42:26  brouard
   int lg=20;    (Module): Bug if status = -2, the loglikelihood was
   i=0;    computed as likelihood omitting the logarithm. Version O.98e
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.118  2006/03/14 18:20:07  brouard
     (s[i] = t[i]);    (Module): varevsij Comments added explaining the second
     if (t[i]== '\\') s[i]='/';    table of variances if popbased=1 .
   }    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 }    (Module): Function pstamp added
     (Module): Version 0.98d
 int nbocc(char *s, char occ)  
 {    Revision 1.117  2006/03/14 17:16:22  brouard
   int i,j=0;    (Module): varevsij Comments added explaining the second
   int lg=20;    table of variances if popbased=1 .
   i=0;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   lg=strlen(s);    (Module): Function pstamp added
   for(i=0; i<= lg; i++) {    (Module): Version 0.98d
   if  (s[i] == occ ) j++;  
   }    Revision 1.116  2006/03/06 10:29:27  brouard
   return j;    (Module): Variance-covariance wrong links and
 }    varian-covariance of ej. is needed (Saito).
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.115  2006/02/27 12:17:45  brouard
 {    (Module): One freematrix added in mlikeli! 0.98c
   int i,lg,j,p=0;  
   i=0;    Revision 1.114  2006/02/26 12:57:58  brouard
   for(j=0; j<=strlen(t)-1; j++) {    (Module): Some improvements in processing parameter
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    filename with strsep.
   }  
     Revision 1.113  2006/02/24 14:20:24  brouard
   lg=strlen(t);    (Module): Memory leaks checks with valgrind and:
   for(j=0; j<p; j++) {    datafile was not closed, some imatrix were not freed and on matrix
     (u[j] = t[j]);    allocation too.
   }  
      u[p]='\0';    Revision 1.112  2006/01/30 09:55:26  brouard
     (Module): Back to gnuplot.exe instead of wgnuplot.exe
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Revision 1.111  2006/01/25 20:38:18  brouard
   }    (Module): Lots of cleaning and bugs added (Gompertz)
 }    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
 /********************** nrerror ********************/  
     Revision 1.110  2006/01/25 00:51:50  brouard
 void nrerror(char error_text[])    (Module): Lots of cleaning and bugs added (Gompertz)
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.109  2006/01/24 19:37:15  brouard
   fprintf(stderr,"%s\n",error_text);    (Module): Comments (lines starting with a #) are allowed in data.
   exit(1);  
 }    Revision 1.108  2006/01/19 18:05:42  lievre
 /*********************** vector *******************/    Gnuplot problem appeared...
 double *vector(int nl, int nh)    To be fixed
 {  
   double *v;    Revision 1.107  2006/01/19 16:20:37  brouard
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Test existence of gnuplot in imach path
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.106  2006/01/19 13:24:36  brouard
 }    Some cleaning and links added in html output
   
 /************************ free vector ******************/    Revision 1.105  2006/01/05 20:23:19  lievre
 void free_vector(double*v, int nl, int nh)    *** empty log message ***
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.104  2005/09/30 16:11:43  lievre
 }    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
 /************************ivector *******************************/    that the person is alive, then we can code his/her status as -2
 int *ivector(long nl,long nh)    (instead of missing=-1 in earlier versions) and his/her
 {    contributions to the likelihood is 1 - Prob of dying from last
   int *v;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    the healthy state at last known wave). Version is 0.98
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;    Revision 1.103  2005/09/30 15:54:49  lievre
 }    (Module): sump fixed, loop imx fixed, and simplifications.
   
 /******************free ivector **************************/    Revision 1.102  2004/09/15 17:31:30  brouard
 void free_ivector(int *v, long nl, long nh)    Add the possibility to read data file including tab characters.
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.101  2004/09/15 10:38:38  brouard
 }    Fix on curr_time
   
 /******************* imatrix *******************************/    Revision 1.100  2004/07/12 18:29:06  brouard
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Add version for Mac OS X. Just define UNIX in Makefile
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    Revision 1.99  2004/06/05 08:57:40  brouard
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    *** empty log message ***
   int **m;  
      Revision 1.98  2004/05/16 15:05:56  brouard
   /* allocate pointers to rows */    New version 0.97 . First attempt to estimate force of mortality
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    directly from the data i.e. without the need of knowing the health
   if (!m) nrerror("allocation failure 1 in matrix()");    state at each age, but using a Gompertz model: log u =a + b*age .
   m += NR_END;    This is the basic analysis of mortality and should be done before any
   m -= nrl;    other analysis, in order to test if the mortality estimated from the
      cross-longitudinal survey is different from the mortality estimated
      from other sources like vital statistic data.
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    The same imach parameter file can be used but the option for mle should be -3.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Agnès, who wrote this part of the code, tried to keep most of the
   m[nrl] -= ncl;    former routines in order to include the new code within the former code.
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    The output is very simple: only an estimate of the intercept and of
      the slope with 95% confident intervals.
   /* return pointer to array of pointers to rows */  
   return m;    Current limitations:
 }    A) Even if you enter covariates, i.e. with the
     model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 /****************** free_imatrix *************************/    B) There is no computation of Life Expectancy nor Life Table.
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    Revision 1.97  2004/02/20 13:25:42  lievre
       long nch,ncl,nrh,nrl;    Version 0.96d. Population forecasting command line is (temporarily)
      /* free an int matrix allocated by imatrix() */    suppressed.
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    Revision 1.96  2003/07/15 15:38:55  brouard
   free((FREE_ARG) (m+nrl-NR_END));    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 }    rewritten within the same printf. Workaround: many printfs.
   
 /******************* matrix *******************************/    Revision 1.95  2003/07/08 07:54:34  brouard
 double **matrix(long nrl, long nrh, long ncl, long nch)    * imach.c (Repository):
 {    (Repository): Using imachwizard code to output a more meaningful covariance
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    matrix (cov(a12,c31) instead of numbers.
   double **m;  
     Revision 1.94  2003/06/27 13:00:02  brouard
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Just cleaning
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.93  2003/06/25 16:33:55  brouard
   m -= nrl;    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): Version 0.96b
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.92  2003/06/25 16:30:45  brouard
   m[nrl] -= ncl;    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;    Revision 1.91  2003/06/25 15:30:29  brouard
 }    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
 /*************************free matrix ************************/    helps to forecast when convergence will be reached. Elapsed time
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    is stamped in powell.  We created a new html file for the graphs
 {    concerning matrix of covariance. It has extension -cov.htm.
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    Revision 1.90  2003/06/24 12:34:15  brouard
 }    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 /******************* ma3x *******************************/    of the covariance matrix to be input.
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {    Revision 1.89  2003/06/24 12:30:52  brouard
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    (Module): Some bugs corrected for windows. Also, when
   double ***m;    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.88  2003/06/23 17:54:56  brouard
   m += NR_END;    * 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.
   m -= nrl;  
     Revision 1.87  2003/06/18 12:26:01  brouard
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Version 0.96
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.86  2003/06/17 20:04:08  brouard
   m[nrl] -= ncl;    (Module): Change position of html and gnuplot routines and added
     routine fileappend.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
     Revision 1.85  2003/06/17 13:12:43  brouard
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    * imach.c (Repository): Check when date of death was earlier that
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    current date of interview. It may happen when the death was just
   m[nrl][ncl] += NR_END;    prior to the death. In this case, dh was negative and likelihood
   m[nrl][ncl] -= nll;    was wrong (infinity). We still send an "Error" but patch by
   for (j=ncl+1; j<=nch; j++)    assuming that the date of death was just one stepm after the
     m[nrl][j]=m[nrl][j-1]+nlay;    interview.
      (Repository): Because some people have very long ID (first column)
   for (i=nrl+1; i<=nrh; i++) {    we changed int to long in num[] and we added a new lvector for
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    memory allocation. But we also truncated to 8 characters (left
     for (j=ncl+1; j<=nch; j++)    truncation)
       m[i][j]=m[i][j-1]+nlay;    (Repository): No more line truncation errors.
   }  
   return m;    Revision 1.84  2003/06/13 21:44:43  brouard
 }    * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
 /*************************free ma3x ************************/    many times. Probs is memory consuming and must be used with
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    parcimony.
 {    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Revision 1.83  2003/06/10 13:39:11  lievre
   free((FREE_ARG)(m+nrl-NR_END));    *** empty log message ***
 }  
     Revision 1.82  2003/06/05 15:57:20  brouard
 /***************** f1dim *************************/    Add log in  imach.c and  fullversion number is now printed.
 extern int ncom;  
 extern double *pcom,*xicom;  */
 extern double (*nrfunc)(double []);  /*
       Interpolated Markov Chain
 double f1dim(double x)  
 {    Short summary of the programme:
   int j;    
   double f;    This program computes Healthy Life Expectancies from
   double *xt;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
      first survey ("cross") where individuals from different ages are
   xt=vector(1,ncom);    interviewed on their health status or degree of disability (in the
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    case of a health survey which is our main interest) -2- at least a
   f=(*nrfunc)(xt);    second wave of interviews ("longitudinal") which measure each change
   free_vector(xt,1,ncom);    (if any) in individual health status.  Health expectancies are
   return f;    computed from the time spent in each health state according to a
 }    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
 /*****************brent *************************/    simplest model is the multinomial logistic model where pij is the
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    probability to be observed in state j at the second wave
 {    conditional to be observed in state i at the first wave. Therefore
   int iter;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   double a,b,d,etemp;    'age' is age and 'sex' is a covariate. If you want to have a more
   double fu,fv,fw,fx;    complex model than "constant and age", you should modify the program
   double ftemp;    where the markup *Covariates have to be included here again* invites
   double p,q,r,tol1,tol2,u,v,w,x,xm;    you to do it.  More covariates you add, slower the
   double e=0.0;    convergence.
    
   a=(ax < cx ? ax : cx);    The advantage of this computer programme, compared to a simple
   b=(ax > cx ? ax : cx);    multinomial logistic model, is clear when the delay between waves is not
   x=w=v=bx;    identical for each individual. Also, if a individual missed an
   fw=fv=fx=(*f)(x);    intermediate interview, the information is lost, but taken into
   for (iter=1;iter<=ITMAX;iter++) {    account using an interpolation or extrapolation.  
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    hPijx is the probability to be observed in state i at age x+h
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    conditional to the observed state i at age x. The delay 'h' can be
     printf(".");fflush(stdout);    split into an exact number (nh*stepm) of unobserved intermediate
 #ifdef DEBUG    states. This elementary transition (by month, quarter,
     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);    semester or year) is modelled as a multinomial logistic.  The hPx
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    matrix is simply the matrix product of nh*stepm elementary matrices
 #endif    and the contribution of each individual to the likelihood is simply
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    hPijx.
       *xmin=x;  
       return fx;    Also this programme outputs the covariance matrix of the parameters but also
     }    of the life expectancies. It also computes the period (stable) prevalence. 
     ftemp=fu;    
     if (fabs(e) > tol1) {    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
       r=(x-w)*(fx-fv);             Institut national d'études démographiques, Paris.
       q=(x-v)*(fx-fw);    This software have been partly granted by Euro-REVES, a concerted action
       p=(x-v)*q-(x-w)*r;    from the European Union.
       q=2.0*(q-r);    It is copyrighted identically to a GNU software product, ie programme and
       if (q > 0.0) p = -p;    software can be distributed freely for non commercial use. Latest version
       q=fabs(q);    can be accessed at http://euroreves.ined.fr/imach .
       etemp=e;  
       e=d;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    
       else {    **********************************************************************/
         d=p/q;  /*
         u=x+d;    main
         if (u-a < tol2 || b-u < tol2)    read parameterfile
           d=SIGN(tol1,xm-x);    read datafile
       }    concatwav
     } else {    freqsummary
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    if (mle >= 1)
     }      mlikeli
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    print results files
     fu=(*f)(u);    if mle==1 
     if (fu <= fx) {       computes hessian
       if (u >= x) a=x; else b=x;    read end of parameter file: agemin, agemax, bage, fage, estepm
       SHFT(v,w,x,u)        begin-prev-date,...
         SHFT(fv,fw,fx,fu)    open gnuplot file
         } else {    open html file
           if (u < x) a=u; else b=u;    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
           if (fu <= fw || w == x) {     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
             v=w;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
             w=u;      freexexit2 possible for memory heap.
             fv=fw;  
             fw=fu;    h Pij x                         | pij_nom  ficrestpij
           } else if (fu <= fv || v == x || v == w) {     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
             v=u;         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
             fv=fu;         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
           }  
         }         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   }         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   nrerror("Too many iterations in brent");    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   *xmin=x;     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   return fx;     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
 }  
     forecasting if prevfcast==1 prevforecast call prevalence()
 /****************** mnbrak ***********************/    health expectancies
     Variance-covariance of DFLE
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    prevalence()
             double (*func)(double))     movingaverage()
 {    varevsij() 
   double ulim,u,r,q, dum;    if popbased==1 varevsij(,popbased)
   double fu;    total life expectancies
      Variance of period (stable) prevalence
   *fa=(*func)(*ax);   end
   *fb=(*func)(*bx);  */
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  
       }   
   *cx=(*bx)+GOLD*(*bx-*ax);  #include <math.h>
   *fc=(*func)(*cx);  #include <stdio.h>
   while (*fb > *fc) {  #include <stdlib.h>
     r=(*bx-*ax)*(*fb-*fc);  #include <string.h>
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #ifdef _WIN32
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #include <io.h>
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #else
     if ((*bx-u)*(u-*cx) > 0.0) {  #include <unistd.h>
       fu=(*func)(u);  #endif
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  #include <limits.h>
       if (fu < *fc) {  #include <sys/types.h>
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #include <sys/stat.h>
           SHFT(*fb,*fc,fu,(*func)(u))  #include <errno.h>
           }  /* extern int errno; */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  /* #ifdef LINUX */
       fu=(*func)(u);  /* #include <time.h> */
     } else {  /* #include "timeval.h" */
       u=(*cx)+GOLD*(*cx-*bx);  /* #else */
       fu=(*func)(u);  /* #include <sys/time.h> */
     }  /* #endif */
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)  #include <time.h>
       }  
 }  #ifdef GSL
   #include <gsl/gsl_errno.h>
 /*************** linmin ************************/  #include <gsl/gsl_multimin.h>
   #endif
 int ncom;  
 double *pcom,*xicom;  #ifdef NLOPT
 double (*nrfunc)(double []);  #include <nlopt.h>
    typedef struct {
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    double (* function)(double [] );
 {  } myfunc_data ;
   double brent(double ax, double bx, double cx,  #endif
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  /* #include <libintl.h> */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /* #define _(String) gettext (String) */
               double *fc, double (*func)(double));  
   int j;  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  #define GNUPLOTPROGRAM "gnuplot"
    /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   ncom=n;  #define FILENAMELENGTH 132
   pcom=vector(1,n);  
   xicom=vector(1,n);  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   nrfunc=func;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
     xicom[j]=xi[j];  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
   }  
   ax=0.0;  #define NINTERVMAX 8
   xx=1.0;  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
 #ifdef DEBUG  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #define MAXN 20000
 #endif  #define YEARM 12. /**< Number of months per year */
   for (j=1;j<=n;j++) {  #define AGESUP 130
     xi[j] *= xmin;  #define AGEBASE 40
     p[j] += xi[j];  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
   }  #ifdef _WIN32
   free_vector(xicom,1,n);  #define DIRSEPARATOR '\\'
   free_vector(pcom,1,n);  #define CHARSEPARATOR "\\"
 }  #define ODIRSEPARATOR '/'
   #else
 /*************** powell ************************/  #define DIRSEPARATOR '/'
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #define CHARSEPARATOR "/"
             double (*func)(double []))  #define ODIRSEPARATOR '\\'
 {  #endif
   void linmin(double p[], double xi[], int n, double *fret,  
               double (*func)(double []));  /* $Id$ */
   int i,ibig,j;  /* $State$ */
   double del,t,*pt,*ptt,*xit;  
   double fp,fptt;  char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
   double *xits;  char fullversion[]="$Revision$ $Date$"; 
   pt=vector(1,n);  char strstart[80];
   ptt=vector(1,n);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   xit=vector(1,n);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   xits=vector(1,n);  int nvar=0, nforce=0; /* Number of variables, number of forces */
   *fret=(*func)(p);  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   for (j=1;j<=n;j++) pt[j]=p[j];  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   for (*iter=1;;++(*iter)) {  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
     fp=(*fret);  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
     ibig=0;  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
     del=0.0;  int cptcovprodnoage=0; /**< Number of covariate products without age */   
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  int cptcoveff=0; /* Total number of covariates to vary for printing results */
     for (i=1;i<=n;i++)  int cptcov=0; /* Working variable */
       printf(" %d %.12f",i, p[i]);  int npar=NPARMAX;
     printf("\n");  int nlstate=2; /* Number of live states */
     for (i=1;i<=n;i++) {  int ndeath=1; /* Number of dead states */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       fptt=(*fret);  int popbased=0;
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  int *wav; /* Number of waves for this individuual 0 is possible */
 #endif  int maxwav=0; /* Maxim number of waves */
       printf("%d",i);fflush(stdout);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
       linmin(p,xit,n,fret,func);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       if (fabs(fptt-(*fret)) > del) {  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
         del=fabs(fptt-(*fret));                     to the likelihood and the sum of weights (done by funcone)*/
         ibig=i;  int mle=1, weightopt=0;
       }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #ifdef DEBUG  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       printf("%d %.12e",i,(*fret));  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       for (j=1;j<=n;j++) {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  int countcallfunc=0;  /* Count the number of calls to func */
         printf(" x(%d)=%.12e",j,xit[j]);  double jmean=1; /* Mean space between 2 waves */
       }  double **matprod2(); /* test */
       for(j=1;j<=n;j++)  double **oldm, **newm, **savm; /* Working pointers to matrices */
         printf(" p=%.12e",p[j]);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       printf("\n");  /*FILE *fic ; */ /* Used in readdata only */
 #endif  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     }  FILE *ficlog, *ficrespow;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  int globpr=0; /* Global variable for printing or not */
 #ifdef DEBUG  double fretone; /* Only one call to likelihood */
       int k[2],l;  long ipmx=0; /* Number of contributions */
       k[0]=1;  double sw; /* Sum of weights */
       k[1]=-1;  char filerespow[FILENAMELENGTH];
       printf("Max: %.12e",(*func)(p));  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       for (j=1;j<=n;j++)  FILE *ficresilk;
         printf(" %.12e",p[j]);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       printf("\n");  FILE *ficresprobmorprev;
       for(l=0;l<=1;l++) {  FILE *fichtm, *fichtmcov; /* Html File */
         for (j=1;j<=n;j++) {  FILE *ficreseij;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  char filerese[FILENAMELENGTH];
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  FILE *ficresstdeij;
         }  char fileresstde[FILENAMELENGTH];
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  FILE *ficrescveij;
       }  char filerescve[FILENAMELENGTH];
 #endif  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
       free_vector(xit,1,n);  char fileresvpl[FILENAMELENGTH];
       free_vector(xits,1,n);  char title[MAXLINE];
       free_vector(ptt,1,n);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       free_vector(pt,1,n);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       return;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     }  char command[FILENAMELENGTH];
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  int  outcmd=0;
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  char filelog[FILENAMELENGTH]; /* Log file */
     }  char filerest[FILENAMELENGTH];
     fptt=(*func)(ptt);  char fileregp[FILENAMELENGTH];
     if (fptt < fp) {  char popfile[FILENAMELENGTH];
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
           xi[j][ibig]=xi[j][n];  /* struct timezone tzp; */
           xi[j][n]=xit[j];  /* extern int gettimeofday(); */
         }  struct tm tml, *gmtime(), *localtime();
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  extern time_t time();
         for(j=1;j<=n;j++)  
           printf(" %.12e",xit[j]);  struct tm start_time, end_time, curr_time, last_time, forecast_time;
         printf("\n");  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
 #endif  struct tm tm;
       }  
     }  char strcurr[80], strfor[80];
   }  
 }  char *endptr;
   long lval;
 /**** Prevalence limit ****************/  double dval;
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  #define NR_END 1
 {  #define FREE_ARG char*
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  #define FTOL 1.0e-10
      matrix by transitions matrix until convergence is reached */  
   #define NRANSI 
   int i, ii,j,k;  #define ITMAX 200 
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();  #define TOL 2.0e-4 
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;  #define CGOLD 0.3819660 
   double agefin, delaymax=50 ; /* Max number of years to converge */  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  #define GOLD 1.618034 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  #define GLIMIT 100.0 
     }  #define TINY 1.0e-20 
   
    cov[1]=1.;  static double maxarg1,maxarg2;
    #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    
     newm=savm;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     /* Covariates have to be included here again */  #define rint(a) floor(a+0.5)
      cov[2]=agefin;  
    static double sqrarg;
       for (k=1; k<=cptcovn;k++) {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  int agegomp= AGEGOMP;
       }  
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  int imx; 
       for (k=1; k<=cptcovprod;k++)  int stepm=1;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /* Stepm, step in month: minimum step interpolation*/
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  int estepm;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  int m,nb;
   long *num;
     savm=oldm;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     oldm=newm;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     maxmax=0.;  double **pmmij, ***probs;
     for(j=1;j<=nlstate;j++){  double *ageexmed,*agecens;
       min=1.;  double dateintmean=0;
       max=0.;  
       for(i=1; i<=nlstate; i++) {  double *weight;
         sumnew=0;  int **s; /* Status */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  double *agedc;
         prlim[i][j]= newm[i][j]/(1-sumnew);  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
         max=FMAX(max,prlim[i][j]);                    * covar=matrix(0,NCOVMAX,1,n); 
         min=FMIN(min,prlim[i][j]);                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       }  double  idx; 
       maxmin=max-min;  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
       maxmax=FMAX(maxmax,maxmin);  int *Ndum; /** Freq of modality (tricode */
     }  int **codtab; /**< codtab=imatrix(1,100,1,10); */
     if(maxmax < ftolpl){  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
       return prlim;  double *lsurv, *lpop, *tpop;
     }  
   }  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
 }  double ftolhess; /**< Tolerance for computing hessian */
   
 /*************** transition probabilities ***************/  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  {
 {    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   double s1, s2;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   /*double t34;*/    */ 
   int i,j,j1, nc, ii, jj;    char  *ss;                            /* pointer */
     int   l1, l2;                         /* length counters */
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){    l1 = strlen(path );                   /* length of path */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
         /*s2 += param[i][j][nc]*cov[nc];*/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    if ( ss == NULL ) {                   /* no directory, so determine current directory */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      strcpy( name, path );               /* we got the fullname name because no directory */
       }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       ps[i][j]=s2;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      /* get current working directory */
     }      /*    extern  char* getcwd ( char *buf , int len);*/
     for(j=i+1; j<=nlstate+ndeath;j++){      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        return( GLOCK_ERROR_GETCWD );
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      }
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      /* got dirc from getcwd*/
       }      printf(" DIRC = %s \n",dirc);
       ps[i][j]=s2;    } else {                              /* strip direcotry from path */
     }      ss++;                               /* after this, the filename */
   }      l2 = strlen( ss );                  /* length of filename */
     /*ps[3][2]=1;*/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
   for(i=1; i<= nlstate; i++){      strncpy( dirc, path, l1 - l2 );     /* now the directory */
      s1=0;      dirc[l1-l2] = 0;                    /* add zero */
     for(j=1; j<i; j++)      printf(" DIRC2 = %s \n",dirc);
       s1+=exp(ps[i][j]);    }
     for(j=i+1; j<=nlstate+ndeath; j++)    /* We add a separator at the end of dirc if not exists */
       s1+=exp(ps[i][j]);    l1 = strlen( dirc );                  /* length of directory */
     ps[i][i]=1./(s1+1.);    if( dirc[l1-1] != DIRSEPARATOR ){
     for(j=1; j<i; j++)      dirc[l1] =  DIRSEPARATOR;
       ps[i][j]= exp(ps[i][j])*ps[i][i];      dirc[l1+1] = 0; 
     for(j=i+1; j<=nlstate+ndeath; j++)      printf(" DIRC3 = %s \n",dirc);
       ps[i][j]= exp(ps[i][j])*ps[i][i];    }
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    ss = strrchr( name, '.' );            /* find last / */
   } /* end i */    if (ss >0){
       ss++;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      strcpy(ext,ss);                     /* save extension */
     for(jj=1; jj<= nlstate+ndeath; jj++){      l1= strlen( name);
       ps[ii][jj]=0;      l2= strlen(ss)+1;
       ps[ii][ii]=1;      strncpy( finame, name, l1-l2);
     }      finame[l1-l2]= 0;
   }    }
   
     return( 0 );                          /* we're done */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  
    }  /******************************************/
     printf("\n ");  
     }  void replace_back_to_slash(char *s, char*t)
     printf("\n ");printf("%lf ",cov[2]);*/  {
 /*    int i;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    int lg=0;
   goto end;*/    i=0;
     return ps;    lg=strlen(t);
 }    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
 /**************** Product of 2 matrices ******************/      if (t[i]== '\\') s[i]='/';
     }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  }
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  char *trimbb(char *out, char *in)
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
   /* in, b, out are matrice of pointers which should have been initialized    char *s;
      before: only the contents of out is modified. The function returns    s=out;
      a pointer to pointers identical to out */    while (*in != '\0'){
   long i, j, k;      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   for(i=nrl; i<= nrh; i++)        in++;
     for(k=ncolol; k<=ncoloh; k++)      }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      *out++ = *in++;
         out[i][k] +=in[i][j]*b[j][k];    }
     *out='\0';
   return out;    return s;
 }  }
   
   char *cutl(char *blocc, char *alocc, char *in, char occ)
 /************* Higher Matrix Product ***************/  {
     /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
 {       gives blocc="abcdef2ghi" and alocc="j".
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month       If occ is not found blocc is null and alocc is equal to in. Returns blocc
      duration (i.e. until    */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    char *s, *t;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    t=in;s=in;
      (typically every 2 years instead of every month which is too big).    while ((*in != occ) && (*in != '\0')){
      Model is determined by parameters x and covariates have to be      *alocc++ = *in++;
      included manually here.    }
     if( *in == occ){
      */      *(alocc)='\0';
       s=++in;
   int i, j, d, h, k;    }
   double **out, cov[NCOVMAX];   
   double **newm;    if (s == t) {/* occ not found */
       *(alocc-(in-s))='\0';
   /* Hstepm could be zero and should return the unit matrix */      in=s;
   for (i=1;i<=nlstate+ndeath;i++)    }
     for (j=1;j<=nlstate+ndeath;j++){    while ( *in != '\0'){
       oldm[i][j]=(i==j ? 1.0 : 0.0);      *blocc++ = *in++;
       po[i][j][0]=(i==j ? 1.0 : 0.0);    }
     }  
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    *blocc='\0';
   for(h=1; h <=nhstepm; h++){    return t;
     for(d=1; d <=hstepm; d++){  }
       newm=savm;  char *cutv(char *blocc, char *alocc, char *in, char occ)
       /* Covariates have to be included here again */  {
       cov[1]=1.;    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];       gives blocc="abcdef2ghi" and alocc="j".
       for (k=1; k<=cptcovage;k++)       If occ is not found blocc is null and alocc is equal to in. Returns alocc
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    */
       for (k=1; k<=cptcovprod;k++)    char *s, *t;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    t=in;s=in;
     while (*in != '\0'){
       while( *in == occ){
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        *blocc++ = *in++;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        s=in;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      *blocc++ = *in++;
       savm=oldm;    }
       oldm=newm;    if (s == t) /* occ not found */
     }      *(blocc-(in-s))='\0';
     for(i=1; i<=nlstate+ndeath; i++)    else
       for(j=1;j<=nlstate+ndeath;j++) {      *(blocc-(in-s)-1)='\0';
         po[i][j][h]=newm[i][j];    in=s;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    while ( *in != '\0'){
          */      *alocc++ = *in++;
       }    }
   } /* end h */  
   return po;    *alocc='\0';
 }    return s;
   }
   
 /*************** log-likelihood *************/  int nbocc(char *s, char occ)
 double func( double *x)  {
 {    int i,j=0;
   int i, ii, j, k, mi, d, kk;    int lg=20;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    i=0;
   double **out;    lg=strlen(s);
   double sw; /* Sum of weights */    for(i=0; i<= lg; i++) {
   double lli; /* Individual log likelihood */    if  (s[i] == occ ) j++;
   long ipmx;    }
   /*extern weight */    return j;
   /* We are differentiating ll according to initial status */  }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)  /* void cutv(char *u,char *v, char*t, char occ) */
     printf(" %d\n",s[4][i]);  /* { */
   */  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   cov[1]=1.;  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   /*      gives u="abcdef2ghi" and v="j" *\/ */
   for(k=1; k<=nlstate; k++) ll[k]=0.;  /*   int i,lg,j,p=0; */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  /*   i=0; */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  /*   lg=strlen(t); */
     for(mi=1; mi<= wav[i]-1; mi++){  /*   for(j=0; j<=lg-1; j++) { */
       for (ii=1;ii<=nlstate+ndeath;ii++)  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /*   } */
       for(d=0; d<dh[mi][i]; d++){  
         newm=savm;  /*   for(j=0; j<p; j++) { */
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  /*     (u[j] = t[j]); */
         for (kk=1; kk<=cptcovage;kk++) {  /*   } */
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  /*      u[p]='\0'; */
         }  
          /*    for(j=0; j<= lg; j++) { */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  /*   } */
         savm=oldm;  /* } */
         oldm=newm;  
          #ifdef _WIN32
          char * strsep(char **pp, const char *delim)
       } /* end mult */  {
          char *p, *q;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);           
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    if ((p = *pp) == NULL)
       ipmx +=1;      return 0;
       sw += weight[i];    if ((q = strpbrk (p, delim)) != NULL)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    {
     } /* end of wave */      *pp = q + 1;
   } /* end of individual */      *q = '\0';
     }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    else
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      *pp = 0;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    return p;
   return -l;  }
 }  #endif
   
   /********************** nrerror ********************/
 /*********** Maximum Likelihood Estimation ***************/  
   void nrerror(char error_text[])
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  {
 {    fprintf(stderr,"ERREUR ...\n");
   int i,j, iter;    fprintf(stderr,"%s\n",error_text);
   double **xi,*delti;    exit(EXIT_FAILURE);
   double fret;  }
   xi=matrix(1,npar,1,npar);  /*********************** vector *******************/
   for (i=1;i<=npar;i++)  double *vector(int nl, int nh)
     for (j=1;j<=npar;j++)  {
       xi[i][j]=(i==j ? 1.0 : 0.0);    double *v;
   printf("Powell\n");    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   powell(p,xi,npar,ftol,&iter,&fret,func);    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
    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));  
   /************************ free vector ******************/
 }  void free_vector(double*v, int nl, int nh)
   {
 /**** Computes Hessian and covariance matrix ***/    free((FREE_ARG)(v+nl-NR_END));
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  }
 {  
   double  **a,**y,*x,pd;  /************************ivector *******************************/
   double **hess;  int *ivector(long nl,long nh)
   int i, j,jk;  {
   int *indx;    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   double hessii(double p[], double delta, int theta, double delti[]);    if (!v) nrerror("allocation failure in ivector");
   double hessij(double p[], double delti[], int i, int j);    return v-nl+NR_END;
   void lubksb(double **a, int npar, int *indx, double b[]) ;  }
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
   /******************free ivector **************************/
   hess=matrix(1,npar,1,npar);  void free_ivector(int *v, long nl, long nh)
   {
   printf("\nCalculation of the hessian matrix. Wait...\n");    free((FREE_ARG)(v+nl-NR_END));
   for (i=1;i<=npar;i++){  }
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);  /************************lvector *******************************/
     /*printf(" %f ",p[i]);*/  long *lvector(long nl,long nh)
     /*printf(" %lf ",hess[i][i]);*/  {
   }    long *v;
      v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   for (i=1;i<=npar;i++) {    if (!v) nrerror("allocation failure in ivector");
     for (j=1;j<=npar;j++)  {    return v-nl+NR_END;
       if (j>i) {  }
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);  /******************free lvector **************************/
         hess[j][i]=hess[i][j];      void free_lvector(long *v, long nl, long nh)
         /*printf(" %lf ",hess[i][j]);*/  {
       }    free((FREE_ARG)(v+nl-NR_END));
     }  }
   }  
   printf("\n");  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
    { 
   a=matrix(1,npar,1,npar);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   y=matrix(1,npar,1,npar);    int **m; 
   x=vector(1,npar);    
   indx=ivector(1,npar);    /* allocate pointers to rows */ 
   for (i=1;i<=npar;i++)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    if (!m) nrerror("allocation failure 1 in matrix()"); 
   ludcmp(a,npar,indx,&pd);    m += NR_END; 
     m -= nrl; 
   for (j=1;j<=npar;j++) {    
     for (i=1;i<=npar;i++) x[i]=0;    
     x[j]=1;    /* allocate rows and set pointers to them */ 
     lubksb(a,npar,indx,x);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     for (i=1;i<=npar;i++){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       matcov[i][j]=x[i];    m[nrl] += NR_END; 
     }    m[nrl] -= ncl; 
   }    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   printf("\n#Hessian matrix#\n");    
   for (i=1;i<=npar;i++) {    /* return pointer to array of pointers to rows */ 
     for (j=1;j<=npar;j++) {    return m; 
       printf("%.3e ",hess[i][j]);  } 
     }  
     printf("\n");  /****************** free_imatrix *************************/
   }  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
   /* Recompute Inverse */        long nch,ncl,nrh,nrl; 
   for (i=1;i<=npar;i++)       /* free an int matrix allocated by imatrix() */ 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  { 
   ludcmp(a,npar,indx,&pd);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
   /*  printf("\n#Hessian matrix recomputed#\n");  } 
   
   for (j=1;j<=npar;j++) {  /******************* matrix *******************************/
     for (i=1;i<=npar;i++) x[i]=0;  double **matrix(long nrl, long nrh, long ncl, long nch)
     x[j]=1;  {
     lubksb(a,npar,indx,x);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     for (i=1;i<=npar;i++){    double **m;
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
     printf("\n");    m += NR_END;
   }    m -= nrl;
   */  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   free_matrix(a,1,npar,1,npar);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   free_matrix(y,1,npar,1,npar);    m[nrl] += NR_END;
   free_vector(x,1,npar);    m[nrl] -= ncl;
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
     /* 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
   that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
 /*************** hessian matrix ****************/     */
 double hessii( double x[], double delta, int theta, double delti[])  }
 {  
   int i;  /*************************free matrix ************************/
   int l=1, lmax=20;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double k1,k2;  {
   double p2[NPARMAX+1];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double res;    free((FREE_ARG)(m+nrl-NR_END));
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  }
   double fx;  
   int k=0,kmax=10;  /******************* ma3x *******************************/
   double l1;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
   fx=func(x);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   for (i=1;i<=npar;i++) p2[i]=x[i];    double ***m;
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     delts=delt;    if (!m) nrerror("allocation failure 1 in matrix()");
     for(k=1 ; k <kmax; k=k+1){    m += NR_END;
       delt = delta*(l1*k);    m -= nrl;
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       p2[theta]=x[theta]-delt;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       k2=func(p2)-fx;    m[nrl] += NR_END;
       /*res= (k1-2.0*fx+k2)/delt/delt; */    m[nrl] -= ncl;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  
          for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 #ifdef DEBUG  
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 #endif    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    m[nrl][ncl] += NR_END;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    m[nrl][ncl] -= nll;
         k=kmax;    for (j=ncl+1; j<=nch; j++) 
       }      m[nrl][j]=m[nrl][j-1]+nlay;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    
         k=kmax; l=lmax*10.;    for (i=nrl+1; i<=nrh; i++) {
       }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      for (j=ncl+1; j<=nch; j++) 
         delts=delt;        m[i][j]=m[i][j-1]+nlay;
       }    }
     }    return m; 
   }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   delti[theta]=delts;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   return res;    */
    }
 }  
   /*************************free ma3x ************************/
 double hessij( double x[], double delti[], int thetai,int thetaj)  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 {  {
   int i;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   int l=1, l1, lmax=20;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double k1,k2,k3,k4,res,fx;    free((FREE_ARG)(m+nrl-NR_END));
   double p2[NPARMAX+1];  }
   int k;  
   /*************** function subdirf ***********/
   fx=func(x);  char *subdirf(char fileres[])
   for (k=1; k<=2; k++) {  {
     for (i=1;i<=npar;i++) p2[i]=x[i];    /* Caution optionfilefiname is hidden */
     p2[thetai]=x[thetai]+delti[thetai]/k;    strcpy(tmpout,optionfilefiname);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    strcat(tmpout,"/"); /* Add to the right */
     k1=func(p2)-fx;    strcat(tmpout,fileres);
      return tmpout;
     p2[thetai]=x[thetai]+delti[thetai]/k;  }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;  /*************** function subdirf2 ***********/
    char *subdirf2(char fileres[], char *preop)
     p2[thetai]=x[thetai]-delti[thetai]/k;  {
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    
     k3=func(p2)-fx;    /* Caution optionfilefiname is hidden */
      strcpy(tmpout,optionfilefiname);
     p2[thetai]=x[thetai]-delti[thetai]/k;    strcat(tmpout,"/");
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    strcat(tmpout,preop);
     k4=func(p2)-fx;    strcat(tmpout,fileres);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    return tmpout;
 #ifdef DEBUG  }
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  
 #endif  /*************** function subdirf3 ***********/
   }  char *subdirf3(char fileres[], char *preop, char *preop2)
   return res;  {
 }    
     /* Caution optionfilefiname is hidden */
 /************** Inverse of matrix **************/    strcpy(tmpout,optionfilefiname);
 void ludcmp(double **a, int n, int *indx, double *d)    strcat(tmpout,"/");
 {    strcat(tmpout,preop);
   int i,imax,j,k;    strcat(tmpout,preop2);
   double big,dum,sum,temp;    strcat(tmpout,fileres);
   double *vv;    return tmpout;
    }
   vv=vector(1,n);  
   *d=1.0;  char *asc_diff_time(long time_sec, char ascdiff[])
   for (i=1;i<=n;i++) {  {
     big=0.0;    long sec_left, days, hours, minutes;
     for (j=1;j<=n;j++)    days = (time_sec) / (60*60*24);
       if ((temp=fabs(a[i][j])) > big) big=temp;    sec_left = (time_sec) % (60*60*24);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    hours = (sec_left) / (60*60) ;
     vv[i]=1.0/big;    sec_left = (sec_left) %(60*60);
   }    minutes = (sec_left) /60;
   for (j=1;j<=n;j++) {    sec_left = (sec_left) % (60);
     for (i=1;i<j;i++) {    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
       sum=a[i][j];    return ascdiff;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  }
       a[i][j]=sum;  
     }  /***************** f1dim *************************/
     big=0.0;  extern int ncom; 
     for (i=j;i<=n;i++) {  extern double *pcom,*xicom;
       sum=a[i][j];  extern double (*nrfunc)(double []); 
       for (k=1;k<j;k++)   
         sum -= a[i][k]*a[k][j];  double f1dim(double x) 
       a[i][j]=sum;  { 
       if ( (dum=vv[i]*fabs(sum)) >= big) {    int j; 
         big=dum;    double f;
         imax=i;    double *xt; 
       }   
     }    xt=vector(1,ncom); 
     if (j != imax) {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       for (k=1;k<=n;k++) {    f=(*nrfunc)(xt); 
         dum=a[imax][k];    free_vector(xt,1,ncom); 
         a[imax][k]=a[j][k];    return f; 
         a[j][k]=dum;  } 
       }  
       *d = -(*d);  /*****************brent *************************/
       vv[imax]=vv[j];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     }  { 
     indx[j]=imax;    int iter; 
     if (a[j][j] == 0.0) a[j][j]=TINY;    double a,b,d,etemp;
     if (j != n) {    double fu=0,fv,fw,fx;
       dum=1.0/(a[j][j]);    double ftemp;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     }    double e=0.0; 
   }   
   free_vector(vv,1,n);  /* Doesn't work */    a=(ax < cx ? ax : cx); 
 ;    b=(ax > cx ? ax : cx); 
 }    x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
 void lubksb(double **a, int n, int *indx, double b[])    for (iter=1;iter<=ITMAX;iter++) { 
 {      xm=0.5*(a+b); 
   int i,ii=0,ip,j;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   double sum;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
        printf(".");fflush(stdout);
   for (i=1;i<=n;i++) {      fprintf(ficlog,".");fflush(ficlog);
     ip=indx[i];  #ifdef DEBUGBRENT
     sum=b[ip];      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);
     b[ip]=b[i];      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 (ii)      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  #endif
     else if (sum) ii=i;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     b[i]=sum;        *xmin=x; 
   }        return fx; 
   for (i=n;i>=1;i--) {      } 
     sum=b[i];      ftemp=fu;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      if (fabs(e) > tol1) { 
     b[i]=sum/a[i][i];        r=(x-w)*(fx-fv); 
   }        q=(x-v)*(fx-fw); 
 }        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
 /************ Frequencies ********************/        if (q > 0.0) p = -p; 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)        q=fabs(q); 
 {  /* Some frequencies */        etemp=e; 
          e=d; 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   double ***freq; /* Frequencies */          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double *pp;        else { 
   double pos, k2, dateintsum=0,k2cpt=0;          d=p/q; 
   FILE *ficresp;          u=x+d; 
   char fileresp[FILENAMELENGTH];          if (u-a < tol2 || b-u < tol2) 
              d=SIGN(tol1,xm-x); 
   pp=vector(1,nlstate);        } 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      } else { 
   strcpy(fileresp,"p");        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   strcat(fileresp,fileres);      } 
   if((ficresp=fopen(fileresp,"w"))==NULL) {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     printf("Problem with prevalence resultfile: %s\n", fileresp);      fu=(*f)(u); 
     exit(0);      if (fu <= fx) { 
   }        if (u >= x) a=x; else b=x; 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        SHFT(v,w,x,u) 
   j1=0;          SHFT(fv,fw,fx,fu) 
            } else { 
   j=cptcoveff;            if (u < x) a=u; else b=u; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            if (fu <= fw || w == x) { 
                v=w; 
   for(k1=1; k1<=j;k1++){              w=u; 
     for(i1=1; i1<=ncodemax[k1];i1++){              fv=fw; 
       j1++;              fw=fu; 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);            } else if (fu <= fv || v == x || v == w) { 
         scanf("%d", i);*/              v=u; 
       for (i=-1; i<=nlstate+ndeath; i++)                fv=fu; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)              } 
           for(m=agemin; m <= agemax+3; m++)          } 
             freq[i][jk][m]=0;    } 
          nrerror("Too many iterations in brent"); 
       dateintsum=0;    *xmin=x; 
       k2cpt=0;    return fx; 
       for (i=1; i<=imx; i++) {  } 
         bool=1;  
         if  (cptcovn>0) {  /****************** mnbrak ***********************/
           for (z1=1; z1<=cptcoveff; z1++)  
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               bool=0;              double (*func)(double)) 
         }  { 
         if (bool==1) {    double ulim,u,r,q, dum;
           for(m=firstpass; m<=lastpass; m++){    double fu; 
             k2=anint[m][i]+(mint[m][i]/12.);   
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    *fa=(*func)(*ax); 
               if(agev[m][i]==0) agev[m][i]=agemax+1;    *fb=(*func)(*bx); 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    if (*fb > *fa) { 
               if (m<lastpass) {      SHFT(dum,*ax,*bx,dum) 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        SHFT(dum,*fb,*fa,dum) 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        } 
               }    *cx=(*bx)+GOLD*(*bx-*ax); 
                  *fc=(*func)(*cx); 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    while (*fb > *fc) { /* Declining fa, fb, fc */
                 dateintsum=dateintsum+k2;      r=(*bx-*ax)*(*fb-*fc); 
                 k2cpt++;      q=(*bx-*cx)*(*fb-*fa); 
               }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
             }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
           }      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
         }      if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
       }        fu=(*func)(u); 
          #ifdef DEBUG
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        /* f(x)=A(x-u)**2+f(u) */
         double A, fparabu; 
       if  (cptcovn>0) {        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
         fprintf(ficresp, "\n#********** Variable ");        fparabu= *fa - A*(*ax-u)*(*ax-u);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
         fprintf(ficresp, "**********\n#");        fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
       }  #endif 
       for(i=1; i<=nlstate;i++)      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        fu=(*func)(u); 
       fprintf(ficresp, "\n");        if (fu < *fc) { 
                SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       for(i=(int)agemin; i <= (int)agemax+3; i++){            SHFT(*fb,*fc,fu,(*func)(u)) 
         if(i==(int)agemax+3)            } 
           printf("Total");      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
         else        u=ulim; 
           printf("Age %d", i);        fu=(*func)(u); 
         for(jk=1; jk <=nlstate ; jk++){      } else { 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        u=(*cx)+GOLD*(*cx-*bx); 
             pp[jk] += freq[jk][m][i];        fu=(*func)(u); 
         }      } 
         for(jk=1; jk <=nlstate ; jk++){      SHFT(*ax,*bx,*cx,u) 
           for(m=-1, pos=0; m <=0 ; m++)        SHFT(*fa,*fb,*fc,fu) 
             pos += freq[jk][m][i];        } 
           if(pp[jk]>=1.e-10)  } 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  
           else  /*************** linmin ************************/
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
         }  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
   and replaces xi by the actual vector displacement that p was moved. Also returns as fret
         for(jk=1; jk <=nlstate ; jk++){  the value of func at the returned location p . This is actually all accomplished by calling the
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  routines mnbrak and brent .*/
             pp[jk] += freq[jk][m][i];  int ncom; 
         }  double *pcom,*xicom;
   double (*nrfunc)(double []); 
         for(jk=1,pos=0; jk <=nlstate ; jk++)   
           pos += pp[jk];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         for(jk=1; jk <=nlstate ; jk++){  { 
           if(pos>=1.e-5)    double brent(double ax, double bx, double cx, 
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);                 double (*f)(double), double tol, double *xmin); 
           else    double f1dim(double x); 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
           if( i <= (int) agemax){                double *fc, double (*func)(double)); 
             if(pos>=1.e-5){    int j; 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    double xx,xmin,bx,ax; 
               probs[i][jk][j1]= pp[jk]/pos;    double fx,fb,fa;
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/   
             }    ncom=n; 
             else    pcom=vector(1,n); 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    xicom=vector(1,n); 
           }    nrfunc=func; 
         }    for (j=1;j<=n;j++) { 
              pcom[j]=p[j]; 
         for(jk=-1; jk <=nlstate+ndeath; jk++)      xicom[j]=xi[j]; 
           for(m=-1; m <=nlstate+ndeath; m++)    } 
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    ax=0.0; 
         if(i <= (int) agemax)    xx=1.0; 
           fprintf(ficresp,"\n");    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
         printf("\n");    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
       }  #ifdef DEBUG
     }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   dateintmean=dateintsum/k2cpt;  #endif
      for (j=1;j<=n;j++) { 
   fclose(ficresp);      xi[j] *= xmin; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      p[j] += xi[j]; 
   free_vector(pp,1,nlstate);    } 
      free_vector(xicom,1,n); 
   /* End of Freq */    free_vector(pcom,1,n); 
 }  } 
   
 /************ Prevalence ********************/  
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)  /*************** powell ************************/
 {  /* Some frequencies */  /*
    Minimization of a function func of n variables. Input consists of an initial starting point
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
   double ***freq; /* Frequencies */  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
   double *pp;  such that failure to decrease by more than this amount on one iteration signals doneness. On
   double pos, k2;  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
   function value at p , and iter is the number of iterations taken. The routine linmin is used.
   pp=vector(1,nlstate);   */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
                double (*func)(double [])) 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  { 
   j1=0;    void linmin(double p[], double xi[], int n, double *fret, 
                  double (*func)(double [])); 
   j=cptcoveff;    int i,ibig,j; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    double del,t,*pt,*ptt,*xit;
      double fp,fptt;
  for(k1=1; k1<=j;k1++){    double *xits;
     for(i1=1; i1<=ncodemax[k1];i1++){    int niterf, itmp;
       j1++;  
      pt=vector(1,n); 
       for (i=-1; i<=nlstate+ndeath; i++)      ptt=vector(1,n); 
         for (jk=-1; jk<=nlstate+ndeath; jk++)      xit=vector(1,n); 
           for(m=agemin; m <= agemax+3; m++)    xits=vector(1,n); 
             freq[i][jk][m]=0;    *fret=(*func)(p); 
          for (j=1;j<=n;j++) pt[j]=p[j]; 
       for (i=1; i<=imx; i++) {      rcurr_time = time(NULL);  
         bool=1;    for (*iter=1;;++(*iter)) { 
         if  (cptcovn>0) {      fp=(*fret); 
           for (z1=1; z1<=cptcoveff; z1++)      ibig=0; 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      del=0.0; 
               bool=0;      rlast_time=rcurr_time;
         }      /* (void) gettimeofday(&curr_time,&tzp); */
         if (bool==1) {      rcurr_time = time(NULL);  
           for(m=firstpass; m<=lastpass; m++){      curr_time = *localtime(&rcurr_time);
             k2=anint[m][i]+(mint[m][i]/12.);      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
               if(agev[m][i]==0) agev[m][i]=agemax+1;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
               if(agev[m][i]==1) agev[m][i]=agemax+2;     for (i=1;i<=n;i++) {
               if (m<lastpass)        printf(" %d %.12f",i, p[i]);
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        fprintf(ficlog," %d %.12lf",i, p[i]);
               else        fprintf(ficrespow," %.12lf", p[i]);
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      }
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];      printf("\n");
             }      fprintf(ficlog,"\n");
           }      fprintf(ficrespow,"\n");fflush(ficrespow);
         }      if(*iter <=3){
       }        tml = *localtime(&rcurr_time);
         for(i=(int)agemin; i <= (int)agemax+3; i++){        strcpy(strcurr,asctime(&tml));
           for(jk=1; jk <=nlstate ; jk++){        rforecast_time=rcurr_time; 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        itmp = strlen(strcurr);
               pp[jk] += freq[jk][m][i];        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           }          strcurr[itmp-1]='\0';
           for(jk=1; jk <=nlstate ; jk++){        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
             for(m=-1, pos=0; m <=0 ; m++)        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
             pos += freq[jk][m][i];        for(niterf=10;niterf<=30;niterf+=10){
         }          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
                  forecast_time = *localtime(&rforecast_time);
          for(jk=1; jk <=nlstate ; jk++){          strcpy(strfor,asctime(&forecast_time));
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          itmp = strlen(strfor);
              pp[jk] += freq[jk][m][i];          if(strfor[itmp-1]=='\n')
          }          strfor[itmp-1]='\0';
                    printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
         }
          for(jk=1; jk <=nlstate ; jk++){                }
            if( i <= (int) agemax){      for (i=1;i<=n;i++) { 
              if(pos>=1.e-5){        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
                probs[i][jk][j1]= pp[jk]/pos;        fptt=(*fret); 
              }  #ifdef DEBUG
            }        printf("fret=%lf \n",*fret);
          }        fprintf(ficlog,"fret=%lf \n",*fret);
            #endif
         }        printf("%d",i);fflush(stdout);
     }        fprintf(ficlog,"%d",i);fflush(ficlog);
   }        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
            del=fabs(fptt-(*fret)); 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          ibig=i; 
   free_vector(pp,1,nlstate);        } 
    #ifdef DEBUG
 }  /* End of Freq */        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
 /************* Waves Concatenation ***************/        for (j=1;j<=n;j++) {
           xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          printf(" x(%d)=%.12e",j,xit[j]);
 {          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        }
      Death is a valid wave (if date is known).        for(j=1;j<=n;j++) {
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          printf(" p(%d)=%.12e",j,p[j]);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
      and mw[mi+1][i]. dh depends on stepm.        }
      */        printf("\n");
         fprintf(ficlog,"\n");
   int i, mi, m;  #endif
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      } /* end i */
      double sum=0., jmean=0.;*/      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
   int j, k=0,jk, ju, jl;        int k[2],l;
   double sum=0.;        k[0]=1;
   jmin=1e+5;        k[1]=-1;
   jmax=-1;        printf("Max: %.12e",(*func)(p));
   jmean=0.;        fprintf(ficlog,"Max: %.12e",(*func)(p));
   for(i=1; i<=imx; i++){        for (j=1;j<=n;j++) {
     mi=0;          printf(" %.12e",p[j]);
     m=firstpass;          fprintf(ficlog," %.12e",p[j]);
     while(s[m][i] <= nlstate){        }
       if(s[m][i]>=1)        printf("\n");
         mw[++mi][i]=m;        fprintf(ficlog,"\n");
       if(m >=lastpass)        for(l=0;l<=1;l++) {
         break;          for (j=1;j<=n;j++) {
       else            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         m++;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     }/* end while */            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     if (s[m][i] > nlstate){          }
       mi++;     /* Death is another wave */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       /* if(mi==0)  never been interviewed correctly before death */          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
          /* Only death is a correct wave */        }
       mw[mi][i]=m;  #endif
     }  
   
     wav[i]=mi;        free_vector(xit,1,n); 
     if(mi==0)        free_vector(xits,1,n); 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        free_vector(ptt,1,n); 
   }        free_vector(pt,1,n); 
         return; 
   for(i=1; i<=imx; i++){      } 
     for(mi=1; mi<wav[i];mi++){      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       if (stepm <=0)      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
         dh[mi][i]=1;        ptt[j]=2.0*p[j]-pt[j]; 
       else{        xit[j]=p[j]-pt[j]; 
         if (s[mw[mi+1][i]][i] > nlstate) {        pt[j]=p[j]; 
           if (agedc[i] < 2*AGESUP) {      } 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      fptt=(*func)(ptt); 
           if(j==0) j=1;  /* Survives at least one month after exam */      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
           k=k+1;        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
           if (j >= jmax) jmax=j;        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
           if (j <= jmin) jmin=j;        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
           sum=sum+j;        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
           }        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
         }        /* Thus we compare delta(2h) with observed f1-f3 */
         else{        /* or best gain on one ancient line 'del' with total  */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        /* gain f1-f2 = f1 - f2 - 'del' with del  */
           k=k+1;        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
           if (j >= jmax) jmax=j;  
           else if (j <= jmin)jmin=j;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        t= t- del*SQR(fp-fptt);
           sum=sum+j;        printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
         }        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
         jk= j/stepm;  #ifdef DEBUG
         jl= j -jk*stepm;        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
         ju= j -(jk+1)*stepm;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         if(jl <= -ju)        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
           dh[mi][i]=jk;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         else        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
           dh[mi][i]=jk+1;        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
         if(dh[mi][i]==0)  #endif
           dh[mi][i]=1; /* At least one step */        if (t < 0.0) { /* Then we use it for last direction */
       }          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
     }          for (j=1;j<=n;j++) { 
   }            xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
   jmean=sum/k;            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          }
  }          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
 /*********** Tricode ****************************/          fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
 void tricode(int *Tvar, int **nbcode, int imx)  
 {  #ifdef DEBUG
   int Ndum[20],ij=1, k, j, i;          for(j=1;j<=n;j++){
   int cptcode=0;            printf(" %.12e",xit[j]);
   cptcoveff=0;            fprintf(ficlog," %.12e",xit[j]);
            }
   for (k=0; k<19; k++) Ndum[k]=0;          printf("\n");
   for (k=1; k<=7; k++) ncodemax[k]=0;          fprintf(ficlog,"\n");
   #endif
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        } /* end of t negative */
     for (i=1; i<=imx; i++) {      } /* end if (fptt < fp)  */
       ij=(int)(covar[Tvar[j]][i]);    } 
       Ndum[ij]++;  } 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  
       if (ij > cptcode) cptcode=ij;  /**** Prevalence limit (stable or period prevalence)  ****************/
     }  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     for (i=0; i<=cptcode; i++) {  {
       if(Ndum[i]!=0) ncodemax[j]++;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     }       matrix by transitions matrix until convergence is reached */
     ij=1;  
     int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
     for (i=1; i<=ncodemax[j]; i++) {    /* double **matprod2(); */ /* test */
       for (k=0; k<=19; k++) {    double **out, cov[NCOVMAX+1], **pmij();
         if (Ndum[k] != 0) {    double **newm;
           nbcode[Tvar[j]][ij]=k;    double agefin, delaymax=50 ; /* Max number of years to converge */
            
           ij++;    for (ii=1;ii<=nlstate+ndeath;ii++)
         }      for (j=1;j<=nlstate+ndeath;j++){
         if (ij > ncodemax[j]) break;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }        }
     }  
   }       cov[1]=1.;
    
  for (k=0; k<19; k++) Ndum[k]=0;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
  for (i=1; i<=ncovmodel-2; i++) {      newm=savm;
       ij=Tvar[i];      /* Covariates have to be included here again */
       Ndum[ij]++;      cov[2]=agefin;
     }      
       for (k=1; k<=cptcovn;k++) {
  ij=1;        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
  for (i=1; i<=10; i++) {        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
    if((Ndum[i]!=0) && (i<=ncovcol)){      }
      Tvaraff[ij]=i;      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
      ij++;      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
    }      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
  }      
        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     cptcoveff=ij-1;      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
 }      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
 /*********** Health Expectancies ****************/      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )      
       savm=oldm;
 {      oldm=newm;
   /* Health expectancies */      maxmax=0.;
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;      for(j=1;j<=nlstate;j++){
   double age, agelim, hf;        min=1.;
   double ***p3mat,***varhe;        max=0.;
   double **dnewm,**doldm;        for(i=1; i<=nlstate; i++) {
   double *xp;          sumnew=0;
   double **gp, **gm;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   double ***gradg, ***trgradg;          prlim[i][j]= newm[i][j]/(1-sumnew);
   int theta;          /*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]);
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          min=FMIN(min,prlim[i][j]);
   xp=vector(1,npar);        }
   dnewm=matrix(1,nlstate*2,1,npar);        maxmin=max-min;
   doldm=matrix(1,nlstate*2,1,nlstate*2);        maxmax=FMAX(maxmax,maxmin);
        }
   fprintf(ficreseij,"# Health expectancies\n");      if(maxmax < ftolpl){
   fprintf(ficreseij,"# Age");        return prlim;
   for(i=1; i<=nlstate;i++)      }
     for(j=1; j<=nlstate;j++)    }
       fprintf(ficreseij," %1d-%1d (SE)",i,j);  }
   fprintf(ficreseij,"\n");  
   /*************** transition probabilities ***************/ 
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   }  {
   else  hstepm=estepm;      /* According to parameters values stored in x and the covariate's values stored in cov,
   /* We compute the life expectancy from trapezoids spaced every estepm months       computes the probability to be observed in state j being in state i by appying the
    * This is mainly to measure the difference between two models: for example       model to the ncovmodel covariates (including constant and age).
    * if stepm=24 months pijx are given only every 2 years and by summing them       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
    * we are calculating an estimate of the Life Expectancy assuming a linear       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
    * progression inbetween and thus overestimating or underestimating according       ncth covariate in the global vector x is given by the formula:
    * to the curvature of the survival function. If, for the same date, we       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
    * estimate the model with stepm=1 month, we can keep estepm to 24 months       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
    * to compare the new estimate of Life expectancy with the same linear       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
    * hypothesis. A more precise result, taking into account a more precise       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
    * curvature will be obtained if estepm is as small as stepm. */       Outputs ps[i][j] the probability to be observed in j being in j according to
        the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   /* 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.    double s1, lnpijopii;
      nhstepm is the number of hstepm from age to agelim    /*double t34;*/
      nstepm is the number of stepm from age to agelin.    int i,j,j1, nc, ii, jj;
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like estepm months */      for(i=1; i<= nlstate; i++){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        for(j=1; j<i;j++){
      survival function given by stepm (the optimization length). Unfortunately it          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
      means that if the survival funtion is printed only each two years of age and if            /*lnpijopii += param[i][j][nc]*cov[nc];*/
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
      results. So we changed our mind and took the option of the best precision.  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   */          }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   agelim=AGESUP;        }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        for(j=i+1; j<=nlstate+ndeath;j++){
     /* nhstepm age range expressed in number of stepm */          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     nstepm=(int) rint((agelim-age)*YEARM/stepm);            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
     /* if (stepm >= YEARM) hstepm=1;*/  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);        }
     gp=matrix(0,nhstepm,1,nlstate*2);      }
     gm=matrix(0,nhstepm,1,nlstate*2);      
       for(i=1; i<= nlstate; i++){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        s1=0;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        for(j=1; j<i; j++){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            s1+=exp(ps[i][j]); /* In fact sums pij/pii */
            /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        for(j=i+1; j<=nlstate+ndeath; j++){
           s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     /* Computing Variances of health expectancies */          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }
      for(theta=1; theta <=npar; theta++){        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       for(i=1; i<=npar; i++){        ps[i][i]=1./(s1+1.);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        /* Computing other pijs */
       }        for(j=1; j<i; j++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            ps[i][j]= exp(ps[i][j])*ps[i][i];
          for(j=i+1; j<=nlstate+ndeath; j++)
       cptj=0;          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=1; j<= nlstate; j++){        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         for(i=1; i<=nlstate; i++){      } /* end i */
           cptj=cptj+1;      
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        for(jj=1; jj<= nlstate+ndeath; jj++){
           }          ps[ii][jj]=0;
         }          ps[ii][ii]=1;
       }        }
            }
            
       for(i=1; i<=npar; i++)      
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
            /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       cptj=0;      /*   } */
       for(j=1; j<= nlstate; j++){      /*   printf("\n "); */
         for(i=1;i<=nlstate;i++){      /* } */
           cptj=cptj+1;      /* printf("\n ");printf("%lf ",cov[2]);*/
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){      /*
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
           }        goto end;*/
         }      return ps;
       }  }
        
      /**************** Product of 2 matrices ******************/
   
       for(j=1; j<= nlstate*2; j++)  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
         for(h=0; h<=nhstepm-1; h++){  {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    /* 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(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
      }       before: only the contents of out is modified. The function returns
           a pointer to pointers identical to out */
 /* End theta */    int i, j, k;
     for(i=nrl; i<= nrh; i++)
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);      for(k=ncolol; k<=ncoloh; k++){
         out[i][k]=0.;
      for(h=0; h<=nhstepm-1; h++)        for(j=ncl; j<=nch; j++)
       for(j=1; j<=nlstate*2;j++)          out[i][k] +=in[i][j]*b[j][k];
         for(theta=1; theta <=npar; theta++)      }
         trgradg[h][j][theta]=gradg[h][theta][j];    return out;
   }
   
      for(i=1;i<=nlstate*2;i++)  
       for(j=1;j<=nlstate*2;j++)  /************* Higher Matrix Product ***************/
         varhe[i][j][(int)age] =0.;  
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     for(h=0;h<=nhstepm-1;h++){  {
       for(k=0;k<=nhstepm-1;k++){    /* Computes the transition matrix starting at age 'age' over 
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);       'nhstepm*hstepm*stepm' months (i.e. until
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         for(i=1;i<=nlstate*2;i++)       nhstepm*hstepm matrices. 
           for(j=1;j<=nlstate*2;j++)       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;       (typically every 2 years instead of every month which is too big 
       }       for the memory).
     }       Model is determined by parameters x and covariates have to be 
        included manually here. 
        
     /* Computing expectancies */       */
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++)    int i, j, d, h, k;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    double **out, cov[NCOVMAX+1];
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    double **newm;
            
 /* 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]);*/    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
         }      for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
     fprintf(ficreseij,"%3.0f",age );        po[i][j][0]=(i==j ? 1.0 : 0.0);
     cptj=0;      }
     for(i=1; i<=nlstate;i++)    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       for(j=1; j<=nlstate;j++){    for(h=1; h <=nhstepm; h++){
         cptj++;      for(d=1; d <=hstepm; d++){
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        newm=savm;
       }        /* Covariates have to be included here again */
     fprintf(ficreseij,"\n");        cov[1]=1.;
            cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     free_matrix(gm,0,nhstepm,1,nlstate*2);        for (k=1; k<=cptcovn;k++) 
     free_matrix(gp,0,nhstepm,1,nlstate*2);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        for (k=1; k<=cptcovage;k++)
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   free_vector(xp,1,npar);  
   free_matrix(dnewm,1,nlstate*2,1,npar);  
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);        /*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, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
 /************ Variance ******************/        savm=oldm;
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)        oldm=newm;
 {      }
   /* Variance of health expectancies */      for(i=1; i<=nlstate+ndeath; i++)
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        for(j=1;j<=nlstate+ndeath;j++) {
   double **newm;          po[i][j][h]=newm[i][j];
   double **dnewm,**doldm;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   int i, j, nhstepm, hstepm, h, nstepm ;        }
   int k, cptcode;      /*printf("h=%d ",h);*/
   double *xp;    } /* end h */
   double **gp, **gm;  /*     printf("\n H=%d \n",h); */
   double ***gradg, ***trgradg;    return po;
   double ***p3mat;  }
   double age,agelim, hf;  
   int theta;  #ifdef NLOPT
     double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
    fprintf(ficresvij,"# Covariances of life expectancies\n");    double fret;
   fprintf(ficresvij,"# Age");    double *xt;
   for(i=1; i<=nlstate;i++)    int j;
     for(j=1; j<=nlstate;j++)    myfunc_data *d2 = (myfunc_data *) pd;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  /* xt = (p1-1); */
   fprintf(ficresvij,"\n");    xt=vector(1,n); 
     for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
   doldm=matrix(1,nlstate,1,nlstate);    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
      printf("Function = %.12lf ",fret);
   if(estepm < stepm){    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     printf ("Problem %d lower than %d\n",estepm, stepm);    printf("\n");
   }   free_vector(xt,1,n);
   else  hstepm=estepm;      return fret;
   /* 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.  #endif
      nhstepm is the number of hstepm from age to agelim  
      nstepm is the number of stepm from age to agelin.  /*************** log-likelihood *************/
      Look at hpijx to understand the reason of that which relies in memory size  double func( double *x)
      and note for a fixed period like k years */  {
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    int i, ii, j, k, mi, d, kk;
      survival function given by stepm (the optimization length). Unfortunately it    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
      means that if the survival funtion is printed only each two years of age and if    double **out;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    double sw; /* Sum of weights */
      results. So we changed our mind and took the option of the best precision.    double lli; /* Individual log likelihood */
   */    int s1, s2;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    double bbh, survp;
   agelim = AGESUP;    long ipmx;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /*extern weight */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    /* We are differentiating ll according to initial status */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*for(i=1;i<imx;i++) 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      printf(" %d\n",s[4][i]);
     gp=matrix(0,nhstepm,1,nlstate);    */
     gm=matrix(0,nhstepm,1,nlstate);  
     ++countcallfunc;
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */    cov[1]=1.;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }    for(k=1; k<=nlstate; k++) ll[k]=0.;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       if (popbased==1) {        /* Computes the values of the ncovmodel covariates of the model
         for(i=1; i<=nlstate;i++)           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
           prlim[i][i]=probs[(int)age][i][ij];           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
       }           to be observed in j being in i according to the model.
           */
       for(j=1; j<= nlstate; j++){        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
         for(h=0; h<=nhstepm; h++){          cov[2+k]=covar[Tvar[k]][i];
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
         }           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
       }           has been calculated etc */
            for(mi=1; mi<= wav[i]-1; mi++){
       for(i=1; i<=npar; i++) /* Computes gradient */          for (ii=1;ii<=nlstate+ndeath;ii++)
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            for (j=1;j<=nlstate+ndeath;j++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
       if (popbased==1) {          for(d=0; d<dh[mi][i]; d++){
         for(i=1; i<=nlstate;i++)            newm=savm;
           prlim[i][i]=probs[(int)age][i][ij];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
       for(j=1; j<= nlstate; j++){            }
         for(h=0; h<=nhstepm; h++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            savm=oldm;
         }            oldm=newm;
       }          } /* end mult */
         
       for(j=1; j<= nlstate; j++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         for(h=0; h<=nhstepm; h++){          /* But now since version 0.9 we anticipate for bias at large stepm.
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         }           * (in months) between two waves is not a multiple of stepm, we rounded to 
     } /* End theta */           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
     for(h=0; h<=nhstepm; h++)           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       for(j=1; j<=nlstate;j++)           * -stepm/2 to stepm/2 .
         for(theta=1; theta <=npar; theta++)           * For stepm=1 the results are the same as for previous versions of Imach.
           trgradg[h][j][theta]=gradg[h][theta][j];           * For stepm > 1 the results are less biased than in previous versions. 
            */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          s1=s[mw[mi][i]][i];
     for(i=1;i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
       for(j=1;j<=nlstate;j++)          bbh=(double)bh[mi][i]/(double)stepm; 
         vareij[i][j][(int)age] =0.;          /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
     for(h=0;h<=nhstepm;h++){           */
       for(k=0;k<=nhstepm;k++){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          if( s2 > nlstate){ 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            /* i.e. if s2 is a death state and if the date of death is known 
         for(i=1;i<=nlstate;i++)               then the contribution to the likelihood is the probability to 
           for(j=1;j<=nlstate;j++)               die between last step unit time and current  step unit time, 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;               which is also equal to probability to die before dh 
       }               minus probability to die before dh-stepm . 
     }               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
     fprintf(ficresvij,"%.0f ",age );          health state: the date of the interview describes the actual state
     for(i=1; i<=nlstate;i++)          and not the date of a change in health state. The former idea was
       for(j=1; j<=nlstate;j++){          to consider that at each interview the state was recorded
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          (healthy, disable or death) and IMaCh was corrected; but when we
       }          introduced the exact date of death then we should have modified
     fprintf(ficresvij,"\n");          the contribution of an exact death to the likelihood. This new
     free_matrix(gp,0,nhstepm,1,nlstate);          contribution is smaller and very dependent of the step unit
     free_matrix(gm,0,nhstepm,1,nlstate);          stepm. It is no more the probability to die between last interview
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          and month of death but the probability to survive from last
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          interview up to one month before death multiplied by the
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          probability to die within a month. Thanks to Chris
   } /* End age */          Jackson for correcting this bug.  Former versions increased
            mortality artificially. The bad side is that we add another loop
   free_vector(xp,1,npar);          which slows down the processing. The difference can be up to 10%
   free_matrix(doldm,1,nlstate,1,npar);          lower mortality.
   free_matrix(dnewm,1,nlstate,1,nlstate);            */
             lli=log(out[s1][s2] - savm[s1][s2]);
 }  
   
 /************ Variance of prevlim ******************/          } else if  (s2==-2) {
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)            for (j=1,survp=0. ; j<=nlstate; j++) 
 {              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   /* Variance of prevalence limit */            /*survp += out[s1][j]; */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            lli= log(survp);
   double **newm;          }
   double **dnewm,**doldm;          
   int i, j, nhstepm, hstepm;          else if  (s2==-4) { 
   int k, cptcode;            for (j=3,survp=0. ; j<=nlstate; j++)  
   double *xp;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double *gp, *gm;            lli= log(survp); 
   double **gradg, **trgradg;          } 
   double age,agelim;  
   int theta;          else if  (s2==-5) { 
                for (j=1,survp=0. ; j<=2; j++)  
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   fprintf(ficresvpl,"# Age");            lli= log(survp); 
   for(i=1; i<=nlstate;i++)          } 
       fprintf(ficresvpl," %1d-%1d",i,i);          
   fprintf(ficresvpl,"\n");          else{
             lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   xp=vector(1,npar);            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   dnewm=matrix(1,nlstate,1,npar);          } 
   doldm=matrix(1,nlstate,1,nlstate);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
            /*if(lli ==000.0)*/
   hstepm=1*YEARM; /* Every year of age */          /*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); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          ipmx +=1;
   agelim = AGESUP;          sw += weight[i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        } /* end of wave */
     if (stepm >= YEARM) hstepm=1;      } /* end of individual */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }  else if(mle==2){
     gradg=matrix(1,npar,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     gp=vector(1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     gm=vector(1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
     for(theta=1; theta <=npar; theta++){            for (j=1;j<=nlstate+ndeath;j++){
       for(i=1; i<=npar; i++){ /* Computes gradient */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for(d=0; d<=dh[mi][i]; d++){
       for(i=1;i<=nlstate;i++)            newm=savm;
         gp[i] = prlim[i][i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                for (kk=1; kk<=cptcovage;kk++) {
       for(i=1; i<=npar; i++) /* Computes gradient */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(i=1;i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         gm[i] = prlim[i][i];            savm=oldm;
             oldm=newm;
       for(i=1;i<=nlstate;i++)          } /* end mult */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        
     } /* End theta */          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     trgradg =matrix(1,nlstate,1,npar);          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(j=1; j<=nlstate;j++)          ipmx +=1;
       for(theta=1; theta <=npar; theta++)          sw += weight[i];
         trgradg[j][theta]=gradg[theta][j];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
     for(i=1;i<=nlstate;i++)      } /* end of individual */
       varpl[i][(int)age] =0.;    }  else if(mle==3){  /* exponential inter-extrapolation */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        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++){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
     fprintf(ficresvpl,"%.0f ",age );              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1; i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            }
     fprintf(ficresvpl,"\n");          for(d=0; d<dh[mi][i]; d++){
     free_vector(gp,1,nlstate);            newm=savm;
     free_vector(gm,1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     free_matrix(gradg,1,npar,1,nlstate);            for (kk=1; kk<=cptcovage;kk++) {
     free_matrix(trgradg,1,nlstate,1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   } /* End age */            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_vector(xp,1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_matrix(doldm,1,nlstate,1,npar);            savm=oldm;
   free_matrix(dnewm,1,nlstate,1,nlstate);            oldm=newm;
           } /* end mult */
 }        
           s1=s[mw[mi][i]][i];
 /************ Variance of one-step probabilities  ******************/          s2=s[mw[mi+1][i]][i];
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          bbh=(double)bh[mi][i]/(double)stepm; 
 {          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 */
   int i, j, i1, k1, j1, z1;          ipmx +=1;
   int k=0, cptcode;          sw += weight[i];
   double **dnewm,**doldm;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double *xp;        } /* end of wave */
   double *gp, *gm;      } /* end of individual */
   double **gradg, **trgradg;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   double age,agelim, cov[NCOVMAX];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int theta;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   char fileresprob[FILENAMELENGTH];        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   strcpy(fileresprob,"prob");            for (j=1;j<=nlstate+ndeath;j++){
   strcat(fileresprob,fileres);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     printf("Problem with resultfile: %s\n", fileresprob);            }
   }          for(d=0; d<dh[mi][i]; d++){
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");            for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficresprob,"# Age");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for(i=1; i<=nlstate;i++)            }
     for(j=1; j<=(nlstate+ndeath);j++)          
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   fprintf(ficresprob,"\n");            oldm=newm;
           } /* end mult */
         
   xp=vector(1,npar);          s1=s[mw[mi][i]][i];
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          s2=s[mw[mi+1][i]][i];
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          if( s2 > nlstate){ 
              lli=log(out[s1][s2] - savm[s1][s2]);
   cov[1]=1;          }else{
   j=cptcoveff;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          }
   j1=0;          ipmx +=1;
   for(k1=1; k1<=1;k1++){          sw += weight[i];
     for(i1=1; i1<=ncodemax[k1];i1++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     j1++;  /*      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 */
     if  (cptcovn>0) {      } /* end of individual */
       fprintf(ficresprob, "\n#********** Variable ");    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       fprintf(ficresprob, "**********\n#");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
              for (ii=1;ii<=nlstate+ndeath;ii++)
       for (age=bage; age<=fage; age ++){            for (j=1;j<=nlstate+ndeath;j++){
         cov[2]=age;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for (k=1; k<=cptcovn;k++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];            }
                    for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for (k=1; k<=cptcovprod;k++)            for (kk=1; kk<=cptcovage;kk++) {
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                    }
         gradg=matrix(1,npar,1,9);          
         trgradg=matrix(1,9,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            savm=oldm;
                oldm=newm;
         for(theta=1; theta <=npar; theta++){          } /* end mult */
           for(i=1; i<=npar; i++)        
             xp[i] = x[i] + (i==theta ?delti[theta]:0);          s1=s[mw[mi][i]][i];
                    s2=s[mw[mi+1][i]][i];
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          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 */
               gp[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]); */
           for(i=1; i<=npar; i++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    return -l;
      }
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  
           k=0;  /*************** log-likelihood *************/
           for(i=1; i<=(nlstate+ndeath); i++){  double funcone( double *x)
             for(j=1; j<=(nlstate+ndeath);j++){  {
               k=k+1;    /* Same as likeli but slower because of a lot of printf and if */
               gm[k]=pmmij[i][j];    int i, ii, j, k, mi, d, kk;
             }    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
           }    double **out;
          double lli; /* Individual log likelihood */
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    double llt;
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      int s1, s2;
         }    double bbh, survp;
     /*extern weight */
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    /* We are differentiating ll according to initial status */
           for(theta=1; theta <=npar; theta++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
             trgradg[j][theta]=gradg[theta][j];    /*for(i=1;i<imx;i++) 
              printf(" %d\n",s[4][i]);
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    */
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    cov[1]=1.;
          
         pmij(pmmij,cov,ncovmodel,x,nlstate);    for(k=1; k<=nlstate; k++) ll[k]=0.;
          
         k=0;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(i=1; i<=(nlstate+ndeath); i++){      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           for(j=1; j<=(nlstate+ndeath);j++){      for(mi=1; mi<= wav[i]-1; mi++){
             k=k+1;        for (ii=1;ii<=nlstate+ndeath;ii++)
             gm[k]=pmmij[i][j];          for (j=1;j<=nlstate+ndeath;j++){
           }            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                }
      /*printf("\n%d ",(int)age);        for(d=0; d<dh[mi][i]; d++){
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          newm=savm;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      }*/          for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         fprintf(ficresprob,"\n%d ",(int)age);          }
           /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
            /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
       }          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
     }          savm=oldm;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          oldm=newm;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        } /* end mult */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        s1=s[mw[mi][i]][i];
   }        s2=s[mw[mi+1][i]][i];
   free_vector(xp,1,npar);        bbh=(double)bh[mi][i]/(double)stepm; 
   fclose(ficresprob);        /* bias is positive if real duration
           * is higher than the multiple of stepm and negative otherwise.
 }         */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
 /******************* Printing html file ***********/          lli=log(out[s1][s2] - savm[s1][s2]);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \        } else if  (s2==-2) {
  int lastpass, int stepm, int weightopt, char model[],\          for (j=1,survp=0. ; j<=nlstate; j++) 
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\          lli= log(survp);
  char version[], int popforecast, int estepm ){        }else if (mle==1){
   int jj1, k1, i1, cpt;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   FILE *fichtm;        } else if(mle==2){
   /*char optionfilehtm[FILENAMELENGTH];*/          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         } else if(mle==3){  /* exponential inter-extrapolation */
   strcpy(optionfilehtm,optionfile);          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   strcat(optionfilehtm,".htm");        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          lli=log(out[s1][s2]); /* Original formula */
     printf("Problem with %s \n",optionfilehtm), exit(0);        } else{  /* mle=0 back to 1 */
   }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*lli=log(out[s1][s2]); */ /* Original formula */
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n        } /* End of if */
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n        ipmx +=1;
 \n        sw += weight[i];
 Total number of observations=%d <br>\n        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n        /*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]); */
 <hr  size=\"2\" color=\"#EC5E5E\">        if(globpr){
  <ul><li>Outputs files<br>\n          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n   %11.6f %11.6f %11.6f ", \
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n            llt +=ll[k]*gipmx/gsw;
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
  fprintf(fichtm,"\n          fprintf(ficresilk," %10.6f\n", -llt);
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n        }
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      } /* end of wave */
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    } /* end of individual */
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
  if(popforecast==1) fprintf(fichtm,"\n    if(globpr==0){ /* First time we count the contributions and weights */
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      gipmx=ipmx;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n      gsw=sw;
         <br>",fileres,fileres,fileres,fileres);    }
  else    return -l;
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);  }
 fprintf(fichtm," <li>Graphs</li><p>");  
   
  m=cptcoveff;  /*************** function likelione ***********/
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
  jj1=0;    /* This routine should help understanding what is done with 
  for(k1=1; k1<=m;k1++){       the selection of individuals/waves and
    for(i1=1; i1<=ncodemax[k1];i1++){       to check the exact contribution to the likelihood.
        jj1++;       Plotting could be done.
        if (cptcovn > 0) {     */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    int k;
          for (cpt=1; cpt<=cptcoveff;cpt++)  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    if(*globpri !=0){ /* Just counts and sums, no printings */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      strcpy(fileresilk,"ilk"); 
        }      strcat(fileresilk,fileres);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            printf("Problem with resultfile: %s\n", fileresilk);
        for(cpt=1; cpt<nlstate;cpt++){        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      }
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      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(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     for(cpt=1; cpt<=nlstate;cpt++) {      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      for(k=1; k<=nlstate; k++) 
 interval) in state (%d): v%s%d%d.gif <br>        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
      }    }
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    *fretone=(*funcone)(p);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    if(*globpri !=0){
      }      fclose(ficresilk);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
 health expectancies in states (1) and (2): e%s%d.gif<br>      fflush(fichtm); 
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    } 
 fprintf(fichtm,"\n</body>");    return;
    }  }
    }  
 fclose(fichtm);  
 }  /*********** Maximum Likelihood Estimation ***************/
   
 /******************* Gnuplot file **************/  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  {
     int i,j, iter;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    double **xi;
     double fret;
   strcpy(optionfilegnuplot,optionfilefiname);    double fretone; /* Only one call to likelihood */
   strcat(optionfilegnuplot,".gp.txt");    /*  char filerespow[FILENAMELENGTH];*/
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);  #ifdef NLOPT
   }    int creturn;
     nlopt_opt opt;
 #ifdef windows    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     fprintf(ficgp,"cd \"%s\" \n",pathc);    double *lb;
 #endif    double minf; /* the minimum objective value, upon return */
 m=pow(2,cptcoveff);    double * p1; /* Shifted parameters from 0 instead of 1 */
      myfunc_data dinst, *d = &dinst;
  /* 1eme*/  #endif
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {  
     xi=matrix(1,npar,1,npar);
 #ifdef windows    for (i=1;i<=npar;i++)
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);      for (j=1;j<=npar;j++)
 #endif        xi[i][j]=(i==j ? 1.0 : 0.0);
 #ifdef unix    printf("Powell\n");  fprintf(ficlog,"Powell\n");
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    strcpy(filerespow,"pow"); 
 #endif    strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
 for (i=1; i<= nlstate ; i ++) {      printf("Problem with resultfile: %s\n", filerespow);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    for (i=1;i<=nlstate;i++)
     for (i=1; i<= nlstate ; i ++) {      for(j=1;j<=nlstate+ndeath;j++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficrespow,"\n");
 }  #ifdef POWELL
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    powell(p,xi,npar,ftol,&iter,&fret,func);
      for (i=1; i<= nlstate ; i ++) {  #endif
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  #ifdef NLOPT
 }    #ifdef NEWUOA
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
 #ifdef unix  #else
 fprintf(ficgp,"\nset ter gif small size 400,300");    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
 #endif  #endif
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    lb=vector(0,npar-1);
    }    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
   }    nlopt_set_lower_bounds(opt, lb);
   /*2 eme*/    nlopt_set_initial_step1(opt, 0.1);
     
   for (k1=1; k1<= m ; k1 ++) {    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    d->function = func;
        printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     for (i=1; i<= nlstate+1 ; i ++) {    nlopt_set_min_objective(opt, myfunc, d);
       k=2*i;    nlopt_set_xtol_rel(opt, ftol);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
       for (j=1; j<= nlstate+1 ; j ++) {      printf("nlopt failed! %d\n",creturn); 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    else {
 }        printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      iter=1; /* not equal */
     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 ++) {    nlopt_destroy(opt);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  #endif
         else fprintf(ficgp," \%%*lf (\%%*lf)");    free_matrix(xi,1,npar,1,npar);
 }      fclose(ficrespow);
       fprintf(ficgp,"\" t\"\" w l 0,");    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
       for (j=1; j<= nlstate+1 ; j ++) {    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  }
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  /**** Computes Hessian and covariance matrix ***/
       else fprintf(ficgp,"\" t\"\" w l 0,");  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     }  {
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    double  **a,**y,*x,pd;
   }    double **hess;
      int i, j,jk;
   /*3eme*/    int *indx;
   
   for (k1=1; k1<= m ; k1 ++) {    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     for (cpt=1; cpt<= nlstate ; cpt ++) {    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       k=2+nlstate*(2*cpt-2);    void lubksb(double **a, int npar, int *indx, double b[]) ;
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    void ludcmp(double **a, int npar, int *indx, double *d) ;
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    double gompertz(double p[]);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    hess=matrix(1,npar,1,npar);
 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);    printf("\nCalculation of the hessian matrix. Wait...\n");
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
 */      fprintf(ficlog,"%d",i);fflush(ficlog);
       for (i=1; i< nlstate ; i ++) {     
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
       }      /*  printf(" %f ",p[i]);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }    }
     }    
      for (i=1;i<=npar;i++) {
   /* CV preval stat */      for (j=1;j<=npar;j++)  {
     for (k1=1; k1<= m ; k1 ++) {        if (j>i) { 
     for (cpt=1; cpt<nlstate ; cpt ++) {          printf(".%d%d",i,j);fflush(stdout);
       k=3;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
       for (i=1; i< nlstate ; i ++)          hess[j][i]=hess[i][j];    
         fprintf(ficgp,"+$%d",k+i+1);          /*printf(" %lf ",hess[i][j]);*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        }
            }
       l=3+(nlstate+ndeath)*cpt;    }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    printf("\n");
       for (i=1; i< nlstate ; i ++) {    fprintf(ficlog,"\n");
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    a=matrix(1,npar,1,npar);
     }    y=matrix(1,npar,1,npar);
   }      x=vector(1,npar);
      indx=ivector(1,npar);
   /* proba elementaires */    for (i=1;i<=npar;i++)
    for(i=1,jk=1; i <=nlstate; i++){      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     for(k=1; k <=(nlstate+ndeath); k++){    ludcmp(a,npar,indx,&pd);
       if (k != i) {  
         for(j=1; j <=ncovmodel; j++){    for (j=1;j<=npar;j++) {
              for (i=1;i<=npar;i++) x[i]=0;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      x[j]=1;
           jk++;      lubksb(a,npar,indx,x);
           fprintf(ficgp,"\n");      for (i=1;i<=npar;i++){ 
         }        matcov[i][j]=x[i];
       }      }
     }    }
     }  
     printf("\n#Hessian matrix#\n");
     for(jk=1; jk <=m; jk++) {    fprintf(ficlog,"\n#Hessian matrix#\n");
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    for (i=1;i<=npar;i++) { 
    i=1;      for (j=1;j<=npar;j++) { 
    for(k2=1; k2<=nlstate; k2++) {        printf("%.3e ",hess[i][j]);
      k3=i;        fprintf(ficlog,"%.3e ",hess[i][j]);
      for(k=1; k<=(nlstate+ndeath); k++) {      }
        if (k != k2){      printf("\n");
         fprintf(ficgp," exp(p%d+p%d*x",i,i+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",i+j-1,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",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /*  printf("\n#Hessian matrix recomputed#\n");
         }  
           fprintf(ficgp,")/(1");    for (j=1;j<=npar;j++) {
              for (i=1;i<=npar;i++) x[i]=0;
         for(k1=1; k1 <=nlstate; k1++){        x[j]=1;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      lubksb(a,npar,indx,x);
 ij=1;      for (i=1;i<=npar;i++){ 
           for(j=3; j <=ncovmodel; j++){        y[i][j]=x[i];
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        printf("%.3e ",y[i][j]);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        fprintf(ficlog,"%.3e ",y[i][j]);
             ij++;      }
           }      printf("\n");
           else      fprintf(ficlog,"\n");
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    }
           }    */
           fprintf(ficgp,")");  
         }    free_matrix(a,1,npar,1,npar);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    free_matrix(y,1,npar,1,npar);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    free_vector(x,1,npar);
         i=i+ncovmodel;    free_ivector(indx,1,npar);
        }    free_matrix(hess,1,npar,1,npar);
      }  
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  }
    }  
      /*************** hessian matrix ****************/
   fclose(ficgp);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 }  /* end gnuplot */  {
     int i;
     int l=1, lmax=20;
 /*************** Moving average **************/    double k1,k2;
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    double p2[MAXPARM+1]; /* identical to x */
     double res;
   int i, cpt, cptcod;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    double fx;
       for (i=1; i<=nlstate;i++)    int k=0,kmax=10;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    double l1;
           mobaverage[(int)agedeb][i][cptcod]=0.;  
        fx=func(x);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    for (i=1;i<=npar;i++) p2[i]=x[i];
       for (i=1; i<=nlstate;i++){    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      l1=pow(10,l);
           for (cpt=0;cpt<=4;cpt++){      delts=delt;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      for(k=1 ; k <kmax; k=k+1){
           }        delt = delta*(l1*k);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        p2[theta]=x[theta] +delt;
         }        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
       }        p2[theta]=x[theta]-delt;
     }        k2=func(p2)-fx;
            /*res= (k1-2.0*fx+k2)/delt/delt; */
 }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
   #ifdef DEBUGHESS
 /************** Forecasting ******************/        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);
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
    #endif
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   int *popage;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          k=kmax;
   double *popeffectif,*popcount;        }
   double ***p3mat;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   char fileresf[FILENAMELENGTH];          k=kmax; l=lmax*10.;
         }
  agelim=AGESUP;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          delts=delt;
         }
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      }
      }
      delti[theta]=delts;
   strcpy(fileresf,"f");    return res; 
   strcat(fileresf,fileres);    
   if((ficresf=fopen(fileresf,"w"))==NULL) {  }
     printf("Problem with forecast resultfile: %s\n", fileresf);  
   }  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   printf("Computing forecasting: result on file '%s' \n", fileresf);  {
     int i;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
   if (mobilav==1) {    double p2[MAXPARM+1];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int k;
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }    fx=func(x);
     for (k=1; k<=2; k++) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;      for (i=1;i<=npar;i++) p2[i]=x[i];
   if (stepm<=12) stepsize=1;      p2[thetai]=x[thetai]+delti[thetai]/k;
        p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   agelim=AGESUP;      k1=func(p2)-fx;
      
   hstepm=1;      p2[thetai]=x[thetai]+delti[thetai]/k;
   hstepm=hstepm/stepm;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   yp1=modf(dateintmean,&yp);      k2=func(p2)-fx;
   anprojmean=yp;    
   yp2=modf((yp1*12),&yp);      p2[thetai]=x[thetai]-delti[thetai]/k;
   mprojmean=yp;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   yp1=modf((yp2*30.5),&yp);      k3=func(p2)-fx;
   jprojmean=yp;    
   if(jprojmean==0) jprojmean=1;      p2[thetai]=x[thetai]-delti[thetai]/k;
   if(mprojmean==0) jprojmean=1;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k4=func(p2)-fx;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
    #ifdef DEBUG
   for(cptcov=1;cptcov<=i2;cptcov++){      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      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);
       k=k+1;  #endif
       fprintf(ficresf,"\n#******");    }
       for(j=1;j<=cptcoveff;j++) {    return res;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  }
       }  
       fprintf(ficresf,"******\n");  /************** Inverse of matrix **************/
       fprintf(ficresf,"# StartingAge FinalAge");  void ludcmp(double **a, int n, int *indx, double *d) 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  { 
          int i,imax,j,k; 
          double big,dum,sum,temp; 
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    double *vv; 
         fprintf(ficresf,"\n");   
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      vv=vector(1,n); 
     *d=1.0; 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    for (i=1;i<=n;i++) { 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      big=0.0; 
           nhstepm = nhstepm/hstepm;      for (j=1;j<=n;j++) 
                  if ((temp=fabs(a[i][j])) > big) big=temp; 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           oldm=oldms;savm=savms;      vv[i]=1.0/big; 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      } 
            for (j=1;j<=n;j++) { 
           for (h=0; h<=nhstepm; h++){      for (i=1;i<j;i++) { 
             if (h==(int) (calagedate+YEARM*cpt)) {        sum=a[i][j]; 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
             }        a[i][j]=sum; 
             for(j=1; j<=nlstate+ndeath;j++) {      } 
               kk1=0.;kk2=0;      big=0.0; 
               for(i=1; i<=nlstate;i++) {                    for (i=j;i<=n;i++) { 
                 if (mobilav==1)        sum=a[i][j]; 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        for (k=1;k<j;k++) 
                 else {          sum -= a[i][k]*a[k][j]; 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        a[i][j]=sum; 
                 }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
                          big=dum; 
               }          imax=i; 
               if (h==(int)(calagedate+12*cpt)){        } 
                 fprintf(ficresf," %.3f", kk1);      } 
                              if (j != imax) { 
               }        for (k=1;k<=n;k++) { 
             }          dum=a[imax][k]; 
           }          a[imax][k]=a[j][k]; 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          a[j][k]=dum; 
         }        } 
       }        *d = -(*d); 
     }        vv[imax]=vv[j]; 
   }      } 
              indx[j]=imax; 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
   fclose(ficresf);        dum=1.0/(a[j][j]); 
 }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
 /************** Forecasting ******************/      } 
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){    } 
      free_vector(vv,1,n);  /* Doesn't work */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  ;
   int *popage;  } 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;  void lubksb(double **a, int n, int *indx, double b[]) 
   double ***p3mat,***tabpop,***tabpopprev;  { 
   char filerespop[FILENAMELENGTH];    int i,ii=0,ip,j; 
     double sum; 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for (i=1;i<=n;i++) { 
   agelim=AGESUP;      ip=indx[i]; 
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      sum=b[ip]; 
        b[ip]=b[i]; 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      if (ii) 
          for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
        else if (sum) ii=i; 
   strcpy(filerespop,"pop");      b[i]=sum; 
   strcat(filerespop,fileres);    } 
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    for (i=n;i>=1;i--) { 
     printf("Problem with forecast resultfile: %s\n", filerespop);      sum=b[i]; 
   }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   printf("Computing forecasting: result on file '%s' \n", filerespop);      b[i]=sum/a[i][i]; 
     } 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  } 
   
   if (mobilav==1) {  void pstamp(FILE *fichier)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  {
     movingaverage(agedeb, fage, ageminpar, mobaverage);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   }  }
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;  /************ Frequencies ********************/
   if (stepm<=12) stepsize=1;  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
    {  /* Some frequencies */
   agelim=AGESUP;    
      int i, m, jk, k1,i1, j1, bool, z1,j;
   hstepm=1;    int first;
   hstepm=hstepm/stepm;    double ***freq; /* Frequencies */
      double *pp, **prop;
   if (popforecast==1) {    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     if((ficpop=fopen(popfile,"r"))==NULL) {    char fileresp[FILENAMELENGTH];
       printf("Problem with population file : %s\n",popfile);exit(0);    
     }    pp=vector(1,nlstate);
     popage=ivector(0,AGESUP);    prop=matrix(1,nlstate,iagemin,iagemax+3);
     popeffectif=vector(0,AGESUP);    strcpy(fileresp,"p");
     popcount=vector(0,AGESUP);    strcat(fileresp,fileres);
        if((ficresp=fopen(fileresp,"w"))==NULL) {
     i=1;        printf("Problem with prevalence resultfile: %s\n", fileresp);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
          exit(0);
     imx=i;    }
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   }    j1=0;
     
   for(cptcov=1;cptcov<=i2;cptcov++){    j=cptcoveff;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       k=k+1;  
       fprintf(ficrespop,"\n#******");    first=1;
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
       }    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
       fprintf(ficrespop,"******\n");    /*    j1++;
       fprintf(ficrespop,"# Age");  */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
       if (popforecast==1)  fprintf(ficrespop," [Population]");        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                scanf("%d", i);*/
       for (cpt=0; cpt<=0;cpt++) {        for (i=-5; i<=nlstate+ndeath; i++)  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            for (jk=-5; jk<=nlstate+ndeath; jk++)  
                    for(m=iagemin; m <= iagemax+3; m++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              freq[i][jk][m]=0;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        
           nhstepm = nhstepm/hstepm;        for (i=1; i<=nlstate; i++)  
                    for(m=iagemin; m <= iagemax+3; m++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            prop[i][m]=0;
           oldm=oldms;savm=savms;        
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          dateintsum=0;
                k2cpt=0;
           for (h=0; h<=nhstepm; h++){        for (i=1; i<=imx; i++) {
             if (h==(int) (calagedate+YEARM*cpt)) {          bool=1;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
             }            for (z1=1; z1<=cptcoveff; z1++)       
             for(j=1; j<=nlstate+ndeath;j++) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
               kk1=0.;kk2=0;                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
               for(i=1; i<=nlstate;i++) {                              bool=0;
                 if (mobilav==1)                /* 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", 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
                 else {                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
                 }              } 
               }          }
               if (h==(int)(calagedate+12*cpt)){   
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          if (bool==1){
                   /*fprintf(ficrespop," %.3f", kk1);            for(m=firstpass; m<=lastpass; m++){
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/              k2=anint[m][i]+(mint[m][i]/12.);
               }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
             }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             for(i=1; i<=nlstate;i++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
               kk1=0.;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                 for(j=1; j<=nlstate;j++){                if (m<lastpass) {
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                 }                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];                }
             }                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)                  dateintsum=dateintsum+k2;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);                  k2cpt++;
           }                }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                /*}*/
         }            }
       }          }
          } /* end i */
   /******/         
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        pstamp(ficresp);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          if  (cptcovn>0) {
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          fprintf(ficresp, "\n#********** Variable "); 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           nhstepm = nhstepm/hstepm;          fprintf(ficresp, "**********\n#");
                    fprintf(ficlog, "\n#********** Variable "); 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           oldm=oldms;savm=savms;          fprintf(ficlog, "**********\n#");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          }
           for (h=0; h<=nhstepm; h++){        for(i=1; i<=nlstate;i++) 
             if (h==(int) (calagedate+YEARM*cpt)) {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        fprintf(ficresp, "\n");
             }        
             for(j=1; j<=nlstate+ndeath;j++) {        for(i=iagemin; i <= iagemax+3; i++){
               kk1=0.;kk2=0;          if(i==iagemax+3){
               for(i=1; i<=nlstate;i++) {                          fprintf(ficlog,"Total");
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              }else{
               }            if(first==1){
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);              first=0;
             }              printf("See log file for details...\n");
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            fprintf(ficlog,"Age %d", i);
         }          }
       }          for(jk=1; jk <=nlstate ; jk++){
    }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   }              pp[jk] += freq[jk][m][i]; 
            }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
   if (popforecast==1) {              pos += freq[jk][m][i];
     free_ivector(popage,0,AGESUP);            if(pp[jk]>=1.e-10){
     free_vector(popeffectif,0,AGESUP);              if(first==1){
     free_vector(popcount,0,AGESUP);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }              }
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }else{
   fclose(ficrespop);              if(first==1)
 }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 /***********************************************/            }
 /**************** Main Program *****************/          }
 /***********************************************/  
           for(jk=1; jk <=nlstate ; jk++){
 int main(int argc, char *argv[])            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 {              pp[jk] += freq[jk][m][i];
           }       
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   double agedeb, agefin,hf;            pos += pp[jk];
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;            posprop += prop[jk][i];
           }
   double fret;          for(jk=1; jk <=nlstate ; jk++){
   double **xi,tmp,delta;            if(pos>=1.e-5){
               if(first==1)
   double dum; /* Dummy variable */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   double ***p3mat;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   int *indx;            }else{
   char line[MAXLINE], linepar[MAXLINE];              if(first==1)
   char title[MAXLINE];                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];            }
              if( i <= iagemax){
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   char filerest[FILENAMELENGTH];                /*probs[i][jk][j1]= pp[jk]/pos;*/
   char fileregp[FILENAMELENGTH];                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   char popfile[FILENAMELENGTH];              }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];              else
   int firstobs=1, lastobs=10;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   int sdeb, sfin; /* Status at beginning and end */            }
   int c,  h , cpt,l;          }
   int ju,jl, mi;          
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          for(jk=-1; jk <=nlstate+ndeath; jk++)
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            for(m=-1; m <=nlstate+ndeath; m++)
   int mobilav=0,popforecast=0;              if(freq[jk][m][i] !=0 ) {
   int hstepm, nhstepm;              if(first==1)
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   double bage, fage, age, agelim, agebase;              }
   double ftolpl=FTOL;          if(i <= iagemax)
   double **prlim;            fprintf(ficresp,"\n");
   double *severity;          if(first==1)
   double ***param; /* Matrix of parameters */            printf("Others in log...\n");
   double  *p;          fprintf(ficlog,"\n");
   double **matcov; /* Matrix of covariance */        }
   double ***delti3; /* Scale */        /*}*/
   double *delti; /* Scale */    }
   double ***eij, ***vareij;    dateintmean=dateintsum/k2cpt; 
   double **varpl; /* Variances of prevalence limits by age */   
   double *epj, vepp;    fclose(ficresp);
   double kk1, kk2;    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    free_vector(pp,1,nlstate);
      free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
   char version[80]="Imach version 0.8a, May 2002, INED-EUROREVES ";  }
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
   /************ Prevalence ********************/
   void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   char z[1]="c", occ;  {  
 #include <sys/time.h>    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
 #include <time.h>       in each health status at the date of interview (if between dateprev1 and dateprev2).
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];       We still use firstpass and lastpass as another selection.
      */
   /* long total_usecs;   
   struct timeval start_time, end_time;    int i, m, jk, k1, i1, j1, bool, z1,j;
      double ***freq; /* Frequencies */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    double *pp, **prop;
   getcwd(pathcd, size);    double pos,posprop; 
     double  y2; /* in fractional years */
   printf("\n%s",version);    int iagemin, iagemax;
   if(argc <=1){    int first; /** to stop verbosity which is redirected to log file */
     printf("\nEnter the parameter file name: ");  
     scanf("%s",pathtot);    iagemin= (int) agemin;
   }    iagemax= (int) agemax;
   else{    /*pp=vector(1,nlstate);*/
     strcpy(pathtot,argv[1]);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    j1=0;
   /*cygwin_split_path(pathtot,path,optionfile);    
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    /*j=cptcoveff;*/
   /* cutv(path,optionfile,pathtot,'\\');*/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    first=1;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
   chdir(path);      /*for(i1=1; i1<=ncodemax[k1];i1++){
   replace(pathc,path);        j1++;*/
         
 /*-------- arguments in the command line --------*/        for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
   strcpy(fileres,"r");            prop[i][m]=0.0;
   strcat(fileres, optionfilefiname);       
   strcat(fileres,".txt");    /* Other files have txt extension */        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
   /*---------arguments file --------*/          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     printf("Problem with optionfile %s\n",optionfile);                bool=0;
     goto end;          } 
   }          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   strcpy(filereso,"o");              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   strcat(filereso,fileres);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   if((ficparo=fopen(filereso,"w"))==NULL) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
   /* Reads comments: lines beginning with '#' */                  /*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]]);*/
   while((c=getc(ficpar))=='#' && c!= EOF){                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     ungetc(c,ficpar);                  prop[s[m][i]][iagemax+3] += weight[i]; 
     fgets(line, MAXLINE, ficpar);                } 
     puts(line);              }
     fputs(line,ficparo);            } /* end selection of waves */
   }          }
   ungetc(c,ficpar);        }
         for(i=iagemin; i <= iagemax+3; i++){  
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   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);            posprop += prop[jk][i]; 
   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);          } 
 while((c=getc(ficpar))=='#' && c!= EOF){          
     ungetc(c,ficpar);          for(jk=1; jk <=nlstate ; jk++){     
     fgets(line, MAXLINE, ficpar);            if( i <=  iagemax){ 
     puts(line);              if(posprop>=1.e-5){ 
     fputs(line,ficparo);                probs[i][jk][j1]= prop[jk][i]/posprop;
   }              } else{
   ungetc(c,ficpar);                if(first==1){
                    first=0;
                      printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
   covar=matrix(0,NCOVMAX,1,n);                }
   cptcovn=0;              }
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;            } 
           }/* end jk */ 
   ncovmodel=2+cptcovn;        }/* end i */ 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      /*} *//* end i1 */
      } /* end j1 */
   /* Read guess parameters */    
   /* Reads comments: lines beginning with '#' */    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   while((c=getc(ficpar))=='#' && c!= EOF){    /*free_vector(pp,1,nlstate);*/
     ungetc(c,ficpar);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     fgets(line, MAXLINE, ficpar);  }  /* End of prevalence */
     puts(line);  
     fputs(line,ficparo);  /************* Waves Concatenation ***************/
   }  
   ungetc(c,ficpar);  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)
    {
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     for(i=1; i <=nlstate; i++)       Death is a valid wave (if date is known).
     for(j=1; j <=nlstate+ndeath-1; j++){       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       fscanf(ficpar,"%1d%1d",&i1,&j1);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       fprintf(ficparo,"%1d%1d",i1,j1);       and mw[mi+1][i]. dh depends on stepm.
       printf("%1d%1d",i,j);       */
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);    int i, mi, m;
         printf(" %lf",param[i][j][k]);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         fprintf(ficparo," %lf",param[i][j][k]);       double sum=0., jmean=0.;*/
       }    int first;
       fscanf(ficpar,"\n");    int j, k=0,jk, ju, jl;
       printf("\n");    double sum=0.;
       fprintf(ficparo,"\n");    first=0;
     }    jmin=1e+5;
      jmax=-1;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    jmean=0.;
     for(i=1; i<=imx; i++){
   p=param[1][1];      mi=0;
        m=firstpass;
   /* Reads comments: lines beginning with '#' */      while(s[m][i] <= nlstate){
   while((c=getc(ficpar))=='#' && c!= EOF){        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     ungetc(c,ficpar);          mw[++mi][i]=m;
     fgets(line, MAXLINE, ficpar);        if(m >=lastpass)
     puts(line);          break;
     fputs(line,ficparo);        else
   }          m++;
   ungetc(c,ficpar);      }/* end while */
       if (s[m][i] > nlstate){
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        mi++;     /* Death is another wave */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        /* if(mi==0)  never been interviewed correctly before death */
   for(i=1; i <=nlstate; i++){           /* Only death is a correct wave */
     for(j=1; j <=nlstate+ndeath-1; j++){        mw[mi][i]=m;
       fscanf(ficpar,"%1d%1d",&i1,&j1);      }
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);      wav[i]=mi;
       for(k=1; k<=ncovmodel;k++){      if(mi==0){
         fscanf(ficpar,"%le",&delti3[i][j][k]);        nbwarn++;
         printf(" %le",delti3[i][j][k]);        if(first==0){
         fprintf(ficparo," %le",delti3[i][j][k]);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       }          first=1;
       fscanf(ficpar,"\n");        }
       printf("\n");        if(first==1){
       fprintf(ficparo,"\n");          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     }        }
   }      } /* end mi==0 */
   delti=delti3[1][1];    } /* End individuals */
    
   /* Reads comments: lines beginning with '#' */    for(i=1; i<=imx; i++){
   while((c=getc(ficpar))=='#' && c!= EOF){      for(mi=1; mi<wav[i];mi++){
     ungetc(c,ficpar);        if (stepm <=0)
     fgets(line, MAXLINE, ficpar);          dh[mi][i]=1;
     puts(line);        else{
     fputs(line,ficparo);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   }            if (agedc[i] < 2*AGESUP) {
   ungetc(c,ficpar);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                if(j==0) j=1;  /* Survives at least one month after exam */
   matcov=matrix(1,npar,1,npar);              else if(j<0){
   for(i=1; i <=npar; i++){                nberr++;
     fscanf(ficpar,"%s",&str);                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]);
     printf("%s",str);                j=1; /* Temporary Dangerous patch */
     fprintf(ficparo,"%s",str);                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(j=1; j <=i; j++){                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fscanf(ficpar," %le",&matcov[i][j]);                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(" %.5le",matcov[i][j]);              }
       fprintf(ficparo," %.5le",matcov[i][j]);              k=k+1;
     }              if (j >= jmax){
     fscanf(ficpar,"\n");                jmax=j;
     printf("\n");                ijmax=i;
     fprintf(ficparo,"\n");              }
   }              if (j <= jmin){
   for(i=1; i <=npar; i++)                jmin=j;
     for(j=i+1;j<=npar;j++)                ijmin=i;
       matcov[i][j]=matcov[j][i];              }
                  sum=sum+j;
   printf("\n");              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
     /*-------- Rewriting paramater file ----------*/          }
      strcpy(rfileres,"r");    /* "Rparameterfile */          else{
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
      strcat(rfileres,".");    /* */  /*        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]); */
      strcat(rfileres,optionfilext);    /* Other files have txt extension */  
     if((ficres =fopen(rfileres,"w"))==NULL) {            k=k+1;
       printf("Problem writing new parameter file: %s\n", fileres);goto end;            if (j >= jmax) {
     }              jmax=j;
     fprintf(ficres,"#%s\n",version);              ijmax=i;
                }
     /*-------- data file ----------*/            else if (j <= jmin){
     if((fic=fopen(datafile,"r"))==NULL)    {              jmin=j;
       printf("Problem with datafile: %s\n", datafile);goto end;              ijmin=i;
     }            }
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     n= lastobs;            /*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]);*/
     severity = vector(1,maxwav);            if(j<0){
     outcome=imatrix(1,maxwav+1,1,n);              nberr++;
     num=ivector(1,n);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     moisnais=vector(1,n);              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     annais=vector(1,n);            }
     moisdc=vector(1,n);            sum=sum+j;
     andc=vector(1,n);          }
     agedc=vector(1,n);          jk= j/stepm;
     cod=ivector(1,n);          jl= j -jk*stepm;
     weight=vector(1,n);          ju= j -(jk+1)*stepm;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     mint=matrix(1,maxwav,1,n);            if(jl==0){
     anint=matrix(1,maxwav,1,n);              dh[mi][i]=jk;
     s=imatrix(1,maxwav+1,1,n);              bh[mi][i]=0;
     adl=imatrix(1,maxwav+1,1,n);                }else{ /* We want a negative bias in order to only have interpolation ie
     tab=ivector(1,NCOVMAX);                    * to avoid the price of an extra matrix product in likelihood */
     ncodemax=ivector(1,8);              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
     i=1;            }
     while (fgets(line, MAXLINE, fic) != NULL)    {          }else{
       if ((i >= firstobs) && (i <=lastobs)) {            if(jl <= -ju){
                      dh[mi][i]=jk;
         for (j=maxwav;j>=1;j--){              bh[mi][i]=jl;       /* bias is positive if real duration
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);                                   * is higher than the multiple of stepm and negative otherwise.
           strcpy(line,stra);                                   */
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            }
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            else{
         }              dh[mi][i]=jk+1;
                      bh[mi][i]=ju;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=ju; /* At least one step */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          } /* end if mle */
         for (j=ncovcol;j>=1;j--){        }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      } /* end wave */
         }    }
         num[i]=atol(stra);    jmean=sum/k;
            printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    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("%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;}*/   }
   
         i=i+1;  /*********** Tricode ****************************/
       }  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
     }  {
     /* printf("ii=%d", ij);    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
        scanf("%d",i);*/    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   imx=i-1; /* Number of individuals */    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
      * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
   /* for (i=1; i<=imx; i++){    /* nbcode[Tvar[j]][1]= 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;  
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     }*/    int modmaxcovj=0; /* Modality max of covariates j */
    /*  for (i=1; i<=imx; i++){    int cptcode=0; /* Modality max of covariates j */
      if (s[4][i]==9)  s[4][i]=-1;    int modmincovj=0; /* Modality min of covariates j */
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/  
    
      cptcoveff=0; 
   /* Calculation of the number of parameter from char model*/   
   Tvar=ivector(1,15);    for (k=-1; k < maxncov; k++) Ndum[k]=0;
   Tprod=ivector(1,15);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   Tvaraff=ivector(1,15);  
   Tvard=imatrix(1,15,1,2);    /* Loop on covariates without age and products */
   Tage=ivector(1,15);          for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
          for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
   if (strlen(model) >1){                                 modality of this covariate Vj*/ 
     j=0, j1=0, k1=1, k2=1;        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
     j=nbocc(model,'+');                                      * If product of Vn*Vm, still boolean *:
     j1=nbocc(model,'*');                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
     cptcovn=j+1;                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
     cptcovprod=j1;        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                            modality of the nth covariate of individual i. */
     strcpy(modelsav,model);        if (ij > modmaxcovj)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          modmaxcovj=ij; 
       printf("Error. Non available option model=%s ",model);        else if (ij < modmincovj) 
       goto end;          modmincovj=ij; 
     }        if ((ij < -1) && (ij > NCOVMAX)){
              printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
     for(i=(j+1); i>=1;i--){          exit(1);
       cutv(stra,strb,modelsav,'+');        }else
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
       /*scanf("%d",i);*/        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       if (strchr(strb,'*')) {        /* getting the maximum value of the modality of the covariate
         cutv(strd,strc,strb,'*');           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
         if (strcmp(strc,"age")==0) {           female is 1, then modmaxcovj=1.*/
           cptcovprod--;      }
           cutv(strb,stre,strd,'V');      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
           Tvar[i]=atoi(stre);      cptcode=modmaxcovj;
           cptcovage++;      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
             Tage[cptcovage]=i;     /*for (i=0; i<=cptcode; i++) {*/
             /*printf("stre=%s ", stre);*/      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]);
         else if (strcmp(strd,"age")==0) {        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           cptcovprod--;          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
           cutv(strb,stre,strc,'V');        }
           Tvar[i]=atoi(stre);        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
           cptcovage++;           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
           Tage[cptcovage]=i;      } /* Ndum[-1] number of undefined modalities */
         }  
         else {      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
           cutv(strb,stre,strc,'V');      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
           Tvar[i]=ncovcol+k1;      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
           cutv(strb,strc,strd,'V');         modmincovj=3; modmaxcovj = 7;
           Tprod[k1]=i;         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
           Tvard[k1][1]=atoi(strc);         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
           Tvard[k1][2]=atoi(stre);         variables V1_1 and V1_2.
           Tvar[cptcovn+k2]=Tvard[k1][1];         nbcode[Tvar[j]][ij]=k;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];         nbcode[Tvar[j]][1]=0;
           for (k=1; k<=lastobs;k++)         nbcode[Tvar[j]][2]=1;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];         nbcode[Tvar[j]][3]=2;
           k1++;      */
           k2=k2+2;      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 */
       }        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
       else {          /*recode from 0 */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
        /*  scanf("%d",i);*/            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
       cutv(strd,strc,strb,'V');                                       k is a modality. If we have model=V1+V1*sex 
       Tvar[i]=atoi(strc);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       }            ij++;
       strcpy(modelsav,stra);            }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          if (ij > ncodemax[j]) break; 
         scanf("%d",i);*/        }  /* end of loop on */
     }      } /* end of loop on modality */ 
 }    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
      
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
   printf("cptcovprod=%d ", cptcovprod);    
   scanf("%d ",i);*/    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
     fclose(fic);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
      ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
     /*  if(mle==1){*/     Ndum[ij]++; 
     if (weightopt != 1) { /* Maximisation without weights*/   } 
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }   ij=1;
     /*-calculation of age at interview from date of interview and age at death -*/   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
     agev=matrix(1,maxwav,1,imx);     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
      if((Ndum[i]!=0) && (i<=ncovcol)){
     for (i=1; i<=imx; i++) {       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
       for(m=2; (m<= maxwav); m++) {       Tvaraff[ij]=i; /*For printing (unclear) */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){       ij++;
          anint[m][i]=9999;     }else
          s[m][i]=-1;         Tvaraff[ij]=0;
        }   }
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;   ij--;
       }   cptcoveff=ij; /*Number of total covariates*/
     }  
   }
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){  /*********** Health Expectancies ****************/
         if(s[m][i] >0){  
           if (s[m][i] >= nlstate+1) {  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)  {
                 agev[m][i]=agedc[i];    /* Health expectancies, no variances */
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
            else {    int nhstepma, nstepma; /* Decreasing with age */
               if (andc[i]!=9999){    double age, agelim, hf;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    double ***p3mat;
               agev[m][i]=-1;    double eip;
               }  
             }    pstamp(ficreseij);
           }    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
           else if(s[m][i] !=9){ /* Should no more exist */    fprintf(ficreseij,"# Age");
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    for(i=1; i<=nlstate;i++){
             if(mint[m][i]==99 || anint[m][i]==9999)      for(j=1; j<=nlstate;j++){
               agev[m][i]=1;        fprintf(ficreseij," e%1d%1d ",i,j);
             else if(agev[m][i] <agemin){      }
               agemin=agev[m][i];      fprintf(ficreseij," e%1d. ",i);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    }
             }    fprintf(ficreseij,"\n");
             else if(agev[m][i] >agemax){  
               agemax=agev[m][i];    
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    if(estepm < stepm){
             }      printf ("Problem %d lower than %d\n",estepm, stepm);
             /*agev[m][i]=anint[m][i]-annais[i];*/    }
             /*   agev[m][i] = age[i]+2*m;*/    else  hstepm=estepm;   
           }    /* We compute the life expectancy from trapezoids spaced every estepm months
           else { /* =9 */     * This is mainly to measure the difference between two models: for example
             agev[m][i]=1;     * if stepm=24 months pijx are given only every 2 years and by summing them
             s[m][i]=-1;     * we are calculating an estimate of the Life Expectancy assuming a linear 
           }     * progression in between and thus overestimating or underestimating according
         }     * to the curvature of the survival function. If, for the same date, we 
         else /*= 0 Unknown */     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           agev[m][i]=1;     * to compare the new estimate of Life expectancy with the same linear 
       }     * hypothesis. A more precise result, taking into account a more precise
         * curvature will be obtained if estepm is as small as stepm. */
     }  
     for (i=1; i<=imx; i++)  {    /* For example we decided to compute the life expectancy with the smallest unit */
       for(m=1; (m<= maxwav); m++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         if (s[m][i] > (nlstate+ndeath)) {       nhstepm is the number of hstepm from age to agelim 
           printf("Error: Wrong value in nlstate or ndeath\n");         nstepm is the number of stepm from age to agelin. 
           goto end;       Look at hpijx to understand the reason of that which relies in memory size
         }       and note for a fixed period like estepm months */
       }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     }       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);       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.
     free_vector(severity,1,maxwav);    */
     free_imatrix(outcome,1,maxwav+1,1,n);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);    agelim=AGESUP;
     /* free_matrix(mint,1,maxwav,1,n);    /* If stepm=6 months */
        free_matrix(anint,1,maxwav,1,n);*/      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     free_vector(moisdc,1,n);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     free_vector(andc,1,n);      
   /* nhstepm age range expressed in number of stepm */
        nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     wav=ivector(1,imx);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    /* if (stepm >= YEARM) hstepm=1;*/
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       Tcode=ivector(1,100);      /* if (stepm >= YEARM) hstepm=1;*/
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       ncodemax[1]=1;  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      /* If stepm=6 months */
            /* Computed by stepm unit matrices, product of hstepma matrices, stored
    codtab=imatrix(1,100,1,10);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
    h=0;      
    m=pow(2,cptcoveff);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
        
    for(k=1;k<=cptcoveff; k++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      for(i=1; i <=(m/pow(2,k));i++){      
        for(j=1; j <= ncodemax[k]; j++){      printf("%d|",(int)age);fflush(stdout);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
            h++;      
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;      /* Computing expectancies */
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/      for(i=1; i<=nlstate;i++)
          }        for(j=1; j<=nlstate;j++)
        }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
      }            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
    }            
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);            /* 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]);*/
       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);      fprintf(ficreseij,"%3.0f",age );
       }      for(i=1; i<=nlstate;i++){
       printf("\n");        eip=0;
       }        for(j=1; j<=nlstate;j++){
       scanf("%d",i);*/          eip +=eij[i][j][(int)age];
              fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
    /* Calculates basic frequencies. Computes observed prevalence at single age        }
        and prints on file fileres'p'. */        fprintf(ficreseij,"%9.4f", eip );
       }
          fprintf(ficreseij,"\n");
          
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    printf("\n");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficlog,"\n");
     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] */  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[] )
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
   {
     if(mle==1){    /* Covariances of health expectancies eij and of total life expectancies according
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);     to initial status i, ei. .
     }    */
        int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     /*--------- results files --------------*/    int nhstepma, nstepma; /* Decreasing with age */
     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);    double age, agelim, hf;
      double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
    jk=1;    double *xp, *xm;
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    double **gp, **gm;
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    double ***gradg, ***trgradg;
    for(i=1,jk=1; i <=nlstate; i++){    int theta;
      for(k=1; k <=(nlstate+ndeath); k++){  
        if (k != i)    double eip, vip;
          {  
            printf("%d%d ",i,k);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
            fprintf(ficres,"%1d%1d ",i,k);    xp=vector(1,npar);
            for(j=1; j <=ncovmodel; j++){    xm=vector(1,npar);
              printf("%f ",p[jk]);    dnewm=matrix(1,nlstate*nlstate,1,npar);
              fprintf(ficres,"%f ",p[jk]);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
              jk++;    
            }    pstamp(ficresstdeij);
            printf("\n");    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
            fprintf(ficres,"\n");    fprintf(ficresstdeij,"# Age");
          }    for(i=1; i<=nlstate;i++){
      }      for(j=1; j<=nlstate;j++)
    }        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
  if(mle==1){      fprintf(ficresstdeij," e%1d. ",i);
     /* Computing hessian and covariance matrix */    }
     ftolhess=ftol; /* Usually correct */    fprintf(ficresstdeij,"\n");
     hesscov(matcov, p, npar, delti, ftolhess, func);  
  }    pstamp(ficrescveij);
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     printf("# Scales (for hessian or gradient estimation)\n");    fprintf(ficrescveij,"# Age");
      for(i=1,jk=1; i <=nlstate; i++){    for(i=1; i<=nlstate;i++)
       for(j=1; j <=nlstate+ndeath; j++){      for(j=1; j<=nlstate;j++){
         if (j!=i) {        cptj= (j-1)*nlstate+i;
           fprintf(ficres,"%1d%1d",i,j);        for(i2=1; i2<=nlstate;i2++)
           printf("%1d%1d",i,j);          for(j2=1; j2<=nlstate;j2++){
           for(k=1; k<=ncovmodel;k++){            cptj2= (j2-1)*nlstate+i2;
             printf(" %.5e",delti[jk]);            if(cptj2 <= cptj)
             fprintf(ficres," %.5e",delti[jk]);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
             jk++;          }
           }      }
           printf("\n");    fprintf(ficrescveij,"\n");
           fprintf(ficres,"\n");    
         }    if(estepm < stepm){
       }      printf ("Problem %d lower than %d\n",estepm, stepm);
      }    }
        else  hstepm=estepm;   
     k=1;    /* We compute the life expectancy from trapezoids spaced every estepm months
     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");     * This is mainly to measure the difference between two models: for example
     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");     * if stepm=24 months pijx are given only every 2 years and by summing them
     for(i=1;i<=npar;i++){     * we are calculating an estimate of the Life Expectancy assuming a linear 
       /*  if (k>nlstate) k=1;     * progression in between and thus overestimating or underestimating according
       i1=(i-1)/(ncovmodel*nlstate)+1;     * to the curvature of the survival function. If, for the same date, we 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       printf("%s%d%d",alph[k],i1,tab[i]);*/     * to compare the new estimate of Life expectancy with the same linear 
       fprintf(ficres,"%3d",i);     * hypothesis. A more precise result, taking into account a more precise
       printf("%3d",i);     * curvature will be obtained if estepm is as small as stepm. */
       for(j=1; j<=i;j++){  
         fprintf(ficres," %.5e",matcov[i][j]);    /* For example we decided to compute the life expectancy with the smallest unit */
         printf(" %.5e",matcov[i][j]);    /* 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 
       fprintf(ficres,"\n");       nstepm is the number of stepm from age to agelin. 
       printf("\n");       Look at hpijx to understand the reason of that which relies in memory size
       k++;       and note for a fixed period like estepm months */
     }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           survival function given by stepm (the optimization length). Unfortunately it
     while((c=getc(ficpar))=='#' && c!= EOF){       means that if the survival funtion is printed only each two years of age and if
       ungetc(c,ficpar);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fgets(line, MAXLINE, ficpar);       results. So we changed our mind and took the option of the best precision.
       puts(line);    */
       fputs(line,ficparo);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     }  
     ungetc(c,ficpar);    /* If stepm=6 months */
     estepm=0;    /* nhstepm age range expressed in number of stepm */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    agelim=AGESUP;
     if (estepm==0 || estepm < stepm) estepm=stepm;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     if (fage <= 2) {    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       bage = ageminpar;    /* if (stepm >= YEARM) hstepm=1;*/
       fage = agemaxpar;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     }    
        p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     while((c=getc(ficpar))=='#' && c!= EOF){    gm=matrix(0,nhstepm,1,nlstate*nlstate);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    for (age=bage; age<=fage; age ++){ 
     puts(line);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     fputs(line,ficparo);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   }      /* if (stepm >= YEARM) hstepm=1;*/
   ungetc(c,ficpar);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
    
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      /* If stepm=6 months */
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
            
   while((c=getc(ficpar))=='#' && c!= EOF){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      /* Computing  Variances of health expectancies */
     puts(line);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     fputs(line,ficparo);         decrease memory allocation */
   }      for(theta=1; theta <=npar; theta++){
   ungetc(c,ficpar);        for(i=1; i<=npar; i++){ 
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        }
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
   fscanf(ficpar,"pop_based=%d\n",&popbased);    
   fprintf(ficparo,"pop_based=%d\n",popbased);          for(j=1; j<= nlstate; j++){
   fprintf(ficres,"pop_based=%d\n",popbased);            for(i=1; i<=nlstate; i++){
              for(h=0; h<=nhstepm-1; h++){
   while((c=getc(ficpar))=='#' && c!= EOF){              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     ungetc(c,ficpar);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
     fgets(line, MAXLINE, ficpar);            }
     puts(line);          }
     fputs(line,ficparo);        }
   }       
   ungetc(c,ficpar);        for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          }
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      }/* End theta */
       
       
 while((c=getc(ficpar))=='#' && c!= EOF){      for(h=0; h<=nhstepm-1; h++)
     ungetc(c,ficpar);        for(j=1; j<=nlstate*nlstate;j++)
     fgets(line, MAXLINE, ficpar);          for(theta=1; theta <=npar; theta++)
     puts(line);            trgradg[h][j][theta]=gradg[h][theta][j];
     fputs(line,ficparo);      
   }  
   ungetc(c,ficpar);       for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);          varhe[ij][ji][(int)age] =0.;
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
 /*------------ gnuplot -------------*/          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
            for(ij=1;ij<=nlstate*nlstate;ij++)
 /*------------ free_vector  -------------*/            for(ji=1;ji<=nlstate*nlstate;ji++)
  chdir(path);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
          }
  free_ivector(wav,1,imx);      }
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        /* Computing expectancies */
  free_ivector(num,1,n);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
  free_vector(agedc,1,n);      for(i=1; i<=nlstate;i++)
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        for(j=1; j<=nlstate;j++)
  fclose(ficparo);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
  fclose(ficres);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
 /*--------- index.htm --------*/            /* 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]);*/
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);          }
   
        fprintf(ficresstdeij,"%3.0f",age );
   /*--------------- Prevalence limit --------------*/      for(i=1; i<=nlstate;i++){
          eip=0.;
   strcpy(filerespl,"pl");        vip=0.;
   strcat(filerespl,fileres);        for(j=1; j<=nlstate;j++){
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          eip += eij[i][j][(int)age];
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   }            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
   fprintf(ficrespl,"#Prevalence limit\n");        }
   fprintf(ficrespl,"#Age ");        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      }
   fprintf(ficrespl,"\n");      fprintf(ficresstdeij,"\n");
    
   prlim=matrix(1,nlstate,1,nlstate);      fprintf(ficrescveij,"%3.0f",age );
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(i=1; i<=nlstate;i++)
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1; j<=nlstate;j++){
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          cptj= (j-1)*nlstate+i;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(i2=1; i2<=nlstate;i2++)
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            for(j2=1; j2<=nlstate;j2++){
   k=0;              cptj2= (j2-1)*nlstate+i2;
   agebase=ageminpar;              if(cptj2 <= cptj)
   agelim=agemaxpar;                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
   ftolpl=1.e-10;            }
   i1=cptcoveff;        }
   if (cptcovn < 1){i1=1;}      fprintf(ficrescveij,"\n");
      
   for(cptcov=1;cptcov<=i1;cptcov++){    }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
         k=k+1;    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
         fprintf(ficrespl,"\n#******");    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
         for(j=1;j<=cptcoveff;j++)    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespl,"******\n");    printf("\n");
            fprintf(ficlog,"\n");
         for (age=agebase; age<=agelim; age++){  
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    free_vector(xm,1,npar);
           fprintf(ficrespl,"%.0f",age );    free_vector(xp,1,npar);
           for(i=1; i<=nlstate;i++)    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
           fprintf(ficrespl," %.5f", prlim[i][i]);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
           fprintf(ficrespl,"\n");    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
         }  }
       }  
     }  /************ Variance ******************/
   fclose(ficrespl);  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[])
   {
   /*------------- h Pij x at various ages ------------*/    /* Variance of health expectancies */
      /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    /* double **newm;*/
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    double **dnewm,**doldm;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    double **dnewmp,**doldmp;
   }    int i, j, nhstepm, hstepm, h, nstepm ;
   printf("Computing pij: result on file '%s' \n", filerespij);    int k, cptcode;
      double *xp;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double **gp, **gm;  /* for var eij */
   /*if (stepm<=24) stepsize=2;*/    double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
   agelim=AGESUP;    double *gpp, *gmp; /* for var p point j */
   hstepm=stepsize*YEARM; /* Every year of age */    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    double ***p3mat;
      double age,agelim, hf;
   k=0;    double ***mobaverage;
   for(cptcov=1;cptcov<=i1;cptcov++){    int theta;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    char digit[4];
       k=k+1;    char digitp[25];
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)    char fileresprobmorprev[FILENAMELENGTH];
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");    if(popbased==1){
              if(mobilav!=0)
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        strcpy(digitp,"-populbased-mobilav-");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      else strcpy(digitp,"-populbased-nomobil-");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    else 
           oldm=oldms;savm=savms;      strcpy(digitp,"-stablbased-");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");    if (mobilav!=0) {
           for(i=1; i<=nlstate;i++)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             for(j=1; j<=nlstate+ndeath;j++)      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
               fprintf(ficrespij," %1d-%1d",i,j);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           fprintf(ficrespij,"\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
            for (h=0; h<=nhstepm; h++){      }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    }
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)    strcpy(fileresprobmorprev,"prmorprev"); 
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    sprintf(digit,"%-d",ij);
             fprintf(ficrespij,"\n");    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
              }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           fprintf(ficrespij,"\n");    strcat(fileresprobmorprev,fileres);
         }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
   fclose(ficrespij);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   /*---------- Forecasting ------------------*/    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   if((stepm == 1) && (strcmp(model,".")==0)){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      fprintf(ficresprobmorprev," p.%-d SE",j);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   else{    }  
     erreur=108;    fprintf(ficresprobmorprev,"\n");
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);    fprintf(ficgp,"\n# Routine varevsij");
   }    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*---------- Health expectancies and variances ------------*/  /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   strcpy(filerest,"t");    pstamp(ficresvij);
   strcat(filerest,fileres);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
   if((ficrest=fopen(filerest,"w"))==NULL) {    if(popbased==1)
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
   }    else
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
   strcpy(filerese,"e");      for(j=1; j<=nlstate;j++)
   strcat(filerese,fileres);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    fprintf(ficresvij,"\n");
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }    xp=vector(1,npar);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
  strcpy(fileresv,"v");    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   strcat(fileresv,fileres);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   }    gpp=vector(nlstate+1,nlstate+ndeath);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    gmp=vector(nlstate+1,nlstate+ndeath);
   calagedate=-1;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    
     if(estepm < stepm){
   k=0;      printf ("Problem %d lower than %d\n",estepm, stepm);
   for(cptcov=1;cptcov<=i1;cptcov++){    }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    else  hstepm=estepm;   
       k=k+1;    /* For example we decided to compute the life expectancy with the smallest unit */
       fprintf(ficrest,"\n#****** ");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       for(j=1;j<=cptcoveff;j++)       nhstepm is the number of hstepm from age to agelim 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       nstepm is the number of stepm from age to agelin. 
       fprintf(ficrest,"******\n");       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
       fprintf(ficreseij,"\n#****** ");       survival function given by stepm (the optimization length). Unfortunately it
       for(j=1;j<=cptcoveff;j++)       means that if the survival funtion is printed every two years of age and if
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fprintf(ficreseij,"******\n");       results. So we changed our mind and took the option of the best precision.
     */
       fprintf(ficresvij,"\n#****** ");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       for(j=1;j<=cptcoveff;j++)    agelim = AGESUP;
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fprintf(ficresvij,"******\n");      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 */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       oldm=oldms;savm=savms;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);        gp=matrix(0,nhstepm,1,nlstate);
        gm=matrix(0,nhstepm,1,nlstate);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;  
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);      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);
          }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fprintf(ficrest,"\n");  
         if (popbased==1) {
       epj=vector(1,nlstate+1);          if(mobilav ==0){
       for(age=bage; age <=fage ;age++){            for(i=1; i<=nlstate;i++)
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);              prlim[i][i]=probs[(int)age][i][ij];
         if (popbased==1) {          }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)            for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][k];              prlim[i][i]=mobaverage[(int)age][i][ij];
         }          }
                }
         fprintf(ficrest," %4.0f",age);    
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        for(j=1; j<= nlstate; j++){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          for(h=0; h<=nhstepm; h++){
             epj[j] += prlim[i][i]*eij[i][j][(int)age];            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }          }
           epj[nlstate+1] +=epj[j];        }
         }        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
         for(i=1, vepp=0.;i <=nlstate;i++)           as a weighted average of prlim.
           for(j=1;j <=nlstate;j++)        */
             vepp += vareij[i][j][(int)age];        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));          for(i=1,gpp[j]=0.; i<= nlstate; i++)
         for(j=1;j <=nlstate;j++){            gpp[j] += prlim[i][i]*p3mat[i][j][1];
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));        }    
         }        /* end probability of death */
         fprintf(ficrest,"\n");  
       }        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);  
 free_matrix(mint,1,maxwav,1,n);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);   
     free_vector(weight,1,n);        if (popbased==1) {
   fclose(ficreseij);          if(mobilav ==0){
   fclose(ficresvij);            for(i=1; i<=nlstate;i++)
   fclose(ficrest);              prlim[i][i]=probs[(int)age][i][ij];
   fclose(ficpar);          }else{ /* mobilav */ 
   free_vector(epj,1,nlstate+1);            for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
   /*------- Variance limit prevalence------*/            }
         }
   strcpy(fileresvpl,"vpl");  
   strcat(fileresvpl,fileres);        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          for(h=0; h<=nhstepm; h++){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     exit(0);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   }          }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        }
         /* This for computing probability of death (h=1 means
   k=0;           computed over hstepm matrices product = hstepm*stepm months) 
   for(cptcov=1;cptcov<=i1;cptcov++){           as a weighted average of prlim.
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        */
       k=k+1;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       fprintf(ficresvpl,"\n#****** ");          for(i=1,gmp[j]=0.; i<= nlstate; i++)
       for(j=1;j<=cptcoveff;j++)           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }    
       fprintf(ficresvpl,"******\n");        /* end probability of death */
        
       varpl=matrix(1,nlstate,(int) bage, (int) fage);        for(j=1; j<= nlstate; j++) /* vareij */
       oldm=oldms;savm=savms;          for(h=0; h<=nhstepm; h++){
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     }          }
  }  
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   fclose(ficresvpl);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      } /* End theta */
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
        for(h=0; h<=nhstepm; h++) /* veij */
          for(j=1; j<=nlstate;j++)
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          for(theta=1; theta <=npar; theta++)
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);            trgradg[h][j][theta]=gradg[h][theta][j];
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
          for(theta=1; theta <=npar; theta++)
   free_matrix(matcov,1,npar,1,npar);          trgradgp[j][theta]=gradgp[theta][j];
   free_vector(delti,1,npar);    
   free_matrix(agev,1,maxwav,1,imx);  
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
   if(erreur >0)        for(j=1;j<=nlstate;j++)
     printf("End of Imach with error or warning %d\n",erreur);          vareij[i][j][(int)age] =0.;
   else   printf("End of Imach\n");  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      for(h=0;h<=nhstepm;h++){
          for(k=0;k<=nhstepm;k++){
   /* 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);*/          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   /*printf("Total time was %d uSec.\n", total_usecs);*/          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   /*------ End -----------*/          for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
  end:        }
 #ifdef windows      }
   /* chdir(pathcd);*/    
 #endif      /* pptj */
  /*system("wgnuplot graph.plt");*/      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
  /*system("../gp37mgw/wgnuplot graph.plt");*/      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
  /*system("cd ../gp37mgw");*/      for(j=nlstate+1;j<=nlstate+ndeath;j++)
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        for(i=nlstate+1;i<=nlstate+ndeath;i++)
  strcpy(plotcmd,GNUPLOTPROGRAM);          varppt[j][i]=doldmp[j][i];
  strcat(plotcmd," ");      /* end ppptj */
  strcat(plotcmd,optionfilegnuplot);      /*  x centered again */
  system(plotcmd);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
 #ifdef windows   
   while (z[0] != 'q') {      if (popbased==1) {
     /* chdir(path); */        if(mobilav ==0){
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");          for(i=1; i<=nlstate;i++)
     scanf("%s",z);            prlim[i][i]=probs[(int)age][i][ij];
     if (z[0] == 'c') system("./imach");        }else{ /* mobilav */ 
     else if (z[0] == 'e') system(optionfilehtm);          for(i=1; i<=nlstate;i++)
     else if (z[0] == 'g') system(plotcmd);            prlim[i][i]=mobaverage[(int)age][i][ij];
     else if (z[0] == 'q') exit(0);        }
   }      }
 #endif               
 }      /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    avoid:
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int i1, j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.41  
changed lines
  Added in v.1.163


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