Diff for /imach/src/imach.c between versions 1.22 and 1.146

version 1.22, 2002/02/22 17:54:20 version 1.146, 2014/06/16 10:20:28
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolate Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.146  2014/06/16 10:20:28  brouard
      Summary: Merge
   This program computes Healthy Life Expectancies from    Author: Brouard
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Merge, before building revised version.
   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 1.145  2014/06/10 21:23:15  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: Debugging with valgrind
   (if any) in individual health status.  Health expectancies are    Author: Nicolas Brouard
   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    Lot of changes in order to output the results with some covariates
   Maximum Likelihood of the parameters involved in the model.  The    After the Edimburgh REVES conference 2014, it seems mandatory to
   simplest model is the multinomial logistic model where pij is the    improve the code.
   probabibility to be observed in state j at the second wave    No more memory valgrind error but a lot has to be done in order to
   conditional to be observed in state i at the first wave. Therefore    continue the work of splitting the code into subroutines.
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Also, decodemodel has been improved. Tricode is still not
   'age' is age and 'sex' is a covariate. If you want to have a more    optimal. nbcode should be improved. Documentation has been added in
   complex model than "constant and age", you should modify the program    the source code.
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.143  2014/01/26 09:45:38  brouard
   convergence.    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   
   The advantage of this computer programme, compared to a simple    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   multinomial logistic model, is clear when the delay between waves is not    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.142  2014/01/26 03:57:36  brouard
   account using an interpolation or extrapolation.      Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   
   hPijx is the probability to be observed in state i at age x+h    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.141  2014/01/26 02:42:01  brouard
   states. This elementary transition (by month or quarter trimester,    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.140  2011/09/02 10:37:54  brouard
   and the contribution of each individual to the likelihood is simply    Summary: times.h is ok with mingw32 now.
   hPijx.  
     Revision 1.139  2010/06/14 07:50:17  brouard
   Also this programme outputs the covariance matrix of the parameters but also    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   of the life expectancies. It also computes the prevalence limits.    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.138  2010/04/30 18:19:40  brouard
            Institut national d'études démographiques, Paris.    *** empty log message ***
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.137  2010/04/29 18:11:38  brouard
   It is copyrighted identically to a GNU software product, ie programme and    (Module): Checking covariates for more complex models
   software can be distributed freely for non commercial use. Latest version    than V1+V2. A lot of change to be done. Unstable.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.136  2010/04/26 20:30:53  brouard
      (Module): merging some libgsl code. Fixing computation
 #include <math.h>    of likelione (using inter/intrapolation if mle = 0) in order to
 #include <stdio.h>    get same likelihood as if mle=1.
 #include <stdlib.h>    Some cleaning of code and comments added.
 #include <unistd.h>  
     Revision 1.135  2009/10/29 15:33:14  brouard
 #define MAXLINE 256    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"  
 #define FILENAMELENGTH 80    Revision 1.134  2009/10/29 13:18:53  brouard
 /*#define DEBUG*/    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.133  2009/07/06 10:21:25  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    just nforces
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.132  2009/07/06 08:22:05  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Many tings
   
 #define NINTERVMAX 8    Revision 1.131  2009/06/20 16:22:47  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Some dimensions resccaled
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.130  2009/05/26 06:44:34  brouard
 #define MAXN 20000    (Module): Max Covariate is now set to 20 instead of 8. A
 #define YEARM 12. /* Number of months per year */    lot of cleaning with variables initialized to 0. Trying to make
 #define AGESUP 130    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 #define AGEBASE 40  
     Revision 1.129  2007/08/31 13:49:27  lievre
     Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 int erreur; /* Error number */  
 int nvar;    Revision 1.128  2006/06/30 13:02:05  brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    (Module): Clarifications on computing e.j
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.127  2006/04/28 18:11:50  brouard
 int ndeath=1; /* Number of dead states */    (Module): Yes the sum of survivors was wrong since
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    imach-114 because nhstepm was no more computed in the age
 int popbased=0;    loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
 int *wav; /* Number of waves for this individuual 0 is possible */    compute health expectancies (without variances) in a first step
 int maxwav; /* Maxim number of waves */    and then all the health expectancies with variances or standard
 int jmin, jmax; /* min, max spacing between 2 waves */    deviation (needs data from the Hessian matrices) which slows the
 int mle, weightopt;    computation.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    In the future we should be able to stop the program is only health
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    expectancies and graph are needed without standard deviations.
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.126  2006/04/28 17:23:28  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): Yes the sum of survivors was wrong since
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    imach-114 because nhstepm was no more computed in the age
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    loop. Now we define nhstepma in the age loop.
 FILE *ficreseij;    Version 0.98h
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Revision 1.125  2006/04/04 15:20:31  lievre
   char fileresv[FILENAMELENGTH];    Errors in calculation of health expectancies. Age was not initialized.
  FILE  *ficresvpl;    Forecasting file added.
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.124  2006/03/22 17:13:53  lievre
 #define NR_END 1    Parameters are printed with %lf instead of %f (more numbers after the comma).
 #define FREE_ARG char*    The log-likelihood is printed in the log file
 #define FTOL 1.0e-10  
     Revision 1.123  2006/03/20 10:52:43  brouard
 #define NRANSI    * imach.c (Module): <title> changed, corresponds to .htm file
 #define ITMAX 200    name. <head> headers where missing.
   
 #define TOL 2.0e-4    * imach.c (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 #define CGOLD 0.3819660    otherwise the weight is truncated).
 #define ZEPS 1.0e-10    Modification of warning when the covariates values are not 0 or
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    1.
     Version 0.98g
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.122  2006/03/20 09:45:41  brouard
 #define TINY 1.0e-20    (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 static double maxarg1,maxarg2;    otherwise the weight is truncated).
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Modification of warning when the covariates values are not 0 or
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    1.
      Version 0.98g
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.121  2006/03/16 17:45:01  lievre
     * imach.c (Module): Comments concerning covariates added
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    * imach.c (Module): refinements in the computation of lli if
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 int imx;  
 int stepm;    Revision 1.120  2006/03/16 15:10:38  lievre
 /* Stepm, step in month: minimum step interpolation*/    (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 int m,nb;    not 1 month. Version 0.98f
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.119  2006/03/15 17:42:26  brouard
 double **pmmij, ***probs, ***mobaverage;    (Module): Bug if status = -2, the loglikelihood was
 double dateintmean=0;    computed as likelihood omitting the logarithm. Version O.98e
   
 double *weight;    Revision 1.118  2006/03/14 18:20:07  brouard
 int **s; /* Status */    (Module): varevsij Comments added explaining the second
 double *agedc, **covar, idx;    table of variances if popbased=1 .
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): Version 0.98d
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.117  2006/03/14 17:16:22  brouard
 /**************** split *************************/    (Module): varevsij Comments added explaining the second
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    table of variances if popbased=1 .
 {    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    char *s;                             /* pointer */    (Module): Function pstamp added
    int  l1, l2;                         /* length counters */    (Module): Version 0.98d
   
    l1 = strlen( path );                 /* length of path */    Revision 1.116  2006/03/06 10:29:27  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): Variance-covariance wrong links and
 #ifdef windows    varian-covariance of ej. is needed (Saito).
    s = strrchr( path, '\\' );           /* find last / */  
 #else    Revision 1.115  2006/02/27 12:17:45  brouard
    s = strrchr( path, '/' );            /* find last / */    (Module): One freematrix added in mlikeli! 0.98c
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */    Revision 1.114  2006/02/26 12:57:58  brouard
 #if     defined(__bsd__)                /* get current working directory */    (Module): Some improvements in processing parameter
       extern char       *getwd( );    filename with strsep.
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.113  2006/02/24 14:20:24  brouard
 #else    (Module): Memory leaks checks with valgrind and:
       extern char       *getcwd( );    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.112  2006/01/30 09:55:26  brouard
          return( GLOCK_ERROR_GETCWD );    (Module): Back to gnuplot.exe instead of wgnuplot.exe
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.111  2006/01/25 20:38:18  brouard
    } else {                             /* strip direcotry from path */    (Module): Lots of cleaning and bugs added (Gompertz)
       s++;                              /* after this, the filename */    (Module): Comments can be added in data file. Missing date values
       l2 = strlen( s );                 /* length of filename */    can be a simple dot '.'.
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.110  2006/01/25 00:51:50  brouard
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    (Module): Lots of cleaning and bugs added (Gompertz)
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.109  2006/01/24 19:37:15  brouard
    l1 = strlen( dirc );                 /* length of directory */    (Module): Comments (lines starting with a #) are allowed in data.
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.108  2006/01/19 18:05:42  lievre
 #else    Gnuplot problem appeared...
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    To be fixed
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.107  2006/01/19 16:20:37  brouard
    s++;    Test existence of gnuplot in imach path
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Revision 1.106  2006/01/19 13:24:36  brouard
    l2= strlen( s)+1;    Some cleaning and links added in html output
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.105  2006/01/05 20:23:19  lievre
    return( 0 );                         /* we're done */    *** empty log message ***
 }  
     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
     that the person is alive, then we can code his/her status as -2
 void replace(char *s, char*t)    (instead of missing=-1 in earlier versions) and his/her
 {    contributions to the likelihood is 1 - Prob of dying from last
   int i;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   int lg=20;    the healthy state at last known wave). Version is 0.98
   i=0;  
   lg=strlen(t);    Revision 1.103  2005/09/30 15:54:49  lievre
   for(i=0; i<= lg; i++) {    (Module): sump fixed, loop imx fixed, and simplifications.
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.102  2004/09/15 17:31:30  brouard
   }    Add the possibility to read data file including tab characters.
 }  
     Revision 1.101  2004/09/15 10:38:38  brouard
 int nbocc(char *s, char occ)    Fix on curr_time
 {  
   int i,j=0;    Revision 1.100  2004/07/12 18:29:06  brouard
   int lg=20;    Add version for Mac OS X. Just define UNIX in Makefile
   i=0;  
   lg=strlen(s);    Revision 1.99  2004/06/05 08:57:40  brouard
   for(i=0; i<= lg; i++) {    *** empty log message ***
   if  (s[i] == occ ) j++;  
   }    Revision 1.98  2004/05/16 15:05:56  brouard
   return j;    New version 0.97 . First attempt to estimate force of mortality
 }    directly from the data i.e. without the need of knowing the health
     state at each age, but using a Gompertz model: log u =a + b*age .
 void cutv(char *u,char *v, char*t, char occ)    This is the basic analysis of mortality and should be done before any
 {    other analysis, in order to test if the mortality estimated from the
   int i,lg,j,p=0;    cross-longitudinal survey is different from the mortality estimated
   i=0;    from other sources like vital statistic data.
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    The same imach parameter file can be used but the option for mle should be -3.
   }  
     Agnès, who wrote this part of the code, tried to keep most of the
   lg=strlen(t);    former routines in order to include the new code within the former code.
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    The output is very simple: only an estimate of the intercept and of
   }    the slope with 95% confident intervals.
      u[p]='\0';  
     Current limitations:
    for(j=0; j<= lg; j++) {    A) Even if you enter covariates, i.e. with the
     if (j>=(p+1))(v[j-p-1] = t[j]);    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   }    B) There is no computation of Life Expectancy nor Life Table.
 }  
     Revision 1.97  2004/02/20 13:25:42  lievre
 /********************** nrerror ********************/    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
 void nrerror(char error_text[])  
 {    Revision 1.96  2003/07/15 15:38:55  brouard
   fprintf(stderr,"ERREUR ...\n");    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   fprintf(stderr,"%s\n",error_text);    rewritten within the same printf. Workaround: many printfs.
   exit(1);  
 }    Revision 1.95  2003/07/08 07:54:34  brouard
 /*********************** vector *******************/    * imach.c (Repository):
 double *vector(int nl, int nh)    (Repository): Using imachwizard code to output a more meaningful covariance
 {    matrix (cov(a12,c31) instead of numbers.
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.94  2003/06/27 13:00:02  brouard
   if (!v) nrerror("allocation failure in vector");    Just cleaning
   return v-nl+NR_END;  
 }    Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 /************************ free vector ******************/    exist so I changed back to asctime which exists.
 void free_vector(double*v, int nl, int nh)    (Module): Version 0.96b
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.92  2003/06/25 16:30:45  brouard
 }    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Revision 1.91  2003/06/25 15:30:29  brouard
 {    * imach.c (Repository): Duplicated warning errors corrected.
   int *v;    (Repository): Elapsed time after each iteration is now output. It
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    helps to forecast when convergence will be reached. Elapsed time
   if (!v) nrerror("allocation failure in ivector");    is stamped in powell.  We created a new html file for the graphs
   return v-nl+NR_END;    concerning matrix of covariance. It has extension -cov.htm.
 }  
     Revision 1.90  2003/06/24 12:34:15  brouard
 /******************free ivector **************************/    (Module): Some bugs corrected for windows. Also, when
 void free_ivector(int *v, long nl, long nh)    mle=-1 a template is output in file "or"mypar.txt with the design
 {    of the covariance matrix to be input.
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
 /******************* imatrix *******************************/    mle=-1 a template is output in file "or"mypar.txt with the design
 int **imatrix(long nrl, long nrh, long ncl, long nch)    of the covariance matrix to be input.
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    Revision 1.88  2003/06/23 17:54:56  brouard
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    * 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.
   int **m;  
      Revision 1.87  2003/06/18 12:26:01  brouard
   /* allocate pointers to rows */    Version 0.96
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.86  2003/06/17 20:04:08  brouard
   m += NR_END;    (Module): Change position of html and gnuplot routines and added
   m -= nrl;    routine fileappend.
    
      Revision 1.85  2003/06/17 13:12:43  brouard
   /* allocate rows and set pointers to them */    * imach.c (Repository): Check when date of death was earlier that
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    current date of interview. It may happen when the death was just
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    prior to the death. In this case, dh was negative and likelihood
   m[nrl] += NR_END;    was wrong (infinity). We still send an "Error" but patch by
   m[nrl] -= ncl;    assuming that the date of death was just one stepm after the
      interview.
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    (Repository): Because some people have very long ID (first column)
      we changed int to long in num[] and we added a new lvector for
   /* return pointer to array of pointers to rows */    memory allocation. But we also truncated to 8 characters (left
   return m;    truncation)
 }    (Repository): No more line truncation errors.
   
 /****************** free_imatrix *************************/    Revision 1.84  2003/06/13 21:44:43  brouard
 void free_imatrix(m,nrl,nrh,ncl,nch)    * imach.c (Repository): Replace "freqsummary" at a correct
       int **m;    place. It differs from routine "prevalence" which may be called
       long nch,ncl,nrh,nrl;    many times. Probs is memory consuming and must be used with
      /* free an int matrix allocated by imatrix() */    parcimony.
 {    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Revision 1.83  2003/06/10 13:39:11  lievre
 }    *** empty log message ***
   
 /******************* matrix *******************************/    Revision 1.82  2003/06/05 15:57:20  brouard
 double **matrix(long nrl, long nrh, long ncl, long nch)    Add log in  imach.c and  fullversion number is now printed.
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  */
   double **m;  /*
      Interpolated Markov Chain
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Short summary of the programme:
   m += NR_END;    
   m -= nrl;    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    first survey ("cross") where individuals from different ages are
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    interviewed on their health status or degree of disability (in the
   m[nrl] += NR_END;    case of a health survey which is our main interest) -2- at least a
   m[nrl] -= ncl;    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    computed from the time spent in each health state according to a
   return m;    model. More health states you consider, more time is necessary to reach the
 }    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
 /*************************free matrix ************************/    probability to be observed in state j at the second wave
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    conditional to be observed in state i at the first wave. Therefore
 {    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    'age' is age and 'sex' is a covariate. If you want to have a more
   free((FREE_ARG)(m+nrl-NR_END));    complex model than "constant and age", you should modify the program
 }    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 /******************* ma3x *******************************/    convergence.
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {    The advantage of this computer programme, compared to a simple
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    multinomial logistic model, is clear when the delay between waves is not
   double ***m;    identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    account using an interpolation or extrapolation.  
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    hPijx is the probability to be observed in state i at age x+h
   m -= nrl;    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    states. This elementary transition (by month, quarter,
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    semester or year) is modelled as a multinomial logistic.  The hPx
   m[nrl] += NR_END;    matrix is simply the matrix product of nh*stepm elementary matrices
   m[nrl] -= ncl;    and the contribution of each individual to the likelihood is simply
     hPijx.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
     Also this programme outputs the covariance matrix of the parameters but also
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    of the life expectancies. It also computes the period (stable) prevalence. 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    
   m[nrl][ncl] += NR_END;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   m[nrl][ncl] -= nll;             Institut national d'études démographiques, Paris.
   for (j=ncl+1; j<=nch; j++)    This software have been partly granted by Euro-REVES, a concerted action
     m[nrl][j]=m[nrl][j-1]+nlay;    from the European Union.
      It is copyrighted identically to a GNU software product, ie programme and
   for (i=nrl+1; i<=nrh; i++) {    software can be distributed freely for non commercial use. Latest version
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    can be accessed at http://euroreves.ined.fr/imach .
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   }    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   return m;    
 }    **********************************************************************/
   /*
 /*************************free ma3x ************************/    main
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    read parameterfile
 {    read datafile
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    concatwav
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    freqsummary
   free((FREE_ARG)(m+nrl-NR_END));    if (mle >= 1)
 }      mlikeli
     print results files
 /***************** f1dim *************************/    if mle==1 
 extern int ncom;       computes hessian
 extern double *pcom,*xicom;    read end of parameter file: agemin, agemax, bage, fage, estepm
 extern double (*nrfunc)(double []);        begin-prev-date,...
      open gnuplot file
 double f1dim(double x)    open html file
 {    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
   int j;     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   double f;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
   double *xt;      freexexit2 possible for memory heap.
    
   xt=vector(1,ncom);    h Pij x                         | pij_nom  ficrestpij
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   f=(*nrfunc)(xt);         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
   free_vector(xt,1,ncom);         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   return f;  
 }         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
 /*****************brent *************************/    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
 {     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   int iter;  
   double a,b,d,etemp;    forecasting if prevfcast==1 prevforecast call prevalence()
   double fu,fv,fw,fx;    health expectancies
   double ftemp;    Variance-covariance of DFLE
   double p,q,r,tol1,tol2,u,v,w,x,xm;    prevalence()
   double e=0.0;     movingaverage()
      varevsij() 
   a=(ax < cx ? ax : cx);    if popbased==1 varevsij(,popbased)
   b=(ax > cx ? ax : cx);    total life expectancies
   x=w=v=bx;    Variance of period (stable) prevalence
   fw=fv=fx=(*f)(x);   end
   for (iter=1;iter<=ITMAX;iter++) {  */
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);   
 #ifdef DEBUG  #include <math.h>
     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);  #include <stdio.h>
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #include <stdlib.h>
 #endif  #include <string.h>
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #include <unistd.h>
       *xmin=x;  
       return fx;  #include <limits.h>
     }  #include <sys/types.h>
     ftemp=fu;  #include <sys/stat.h>
     if (fabs(e) > tol1) {  #include <errno.h>
       r=(x-w)*(fx-fv);  extern int errno;
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;  #ifdef LINUX
       q=2.0*(q-r);  #include <time.h>
       if (q > 0.0) p = -p;  #include "timeval.h"
       q=fabs(q);  #else
       etemp=e;  #include <sys/time.h>
       e=d;  #endif
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  #ifdef GSL
       else {  #include <gsl/gsl_errno.h>
         d=p/q;  #include <gsl/gsl_multimin.h>
         u=x+d;  #endif
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  /* #include <libintl.h> */
       }  /* #define _(String) gettext (String) */
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #define GNUPLOTPROGRAM "gnuplot"
     fu=(*f)(u);  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     if (fu <= fx) {  #define FILENAMELENGTH 132
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
         SHFT(fv,fw,fx,fu)  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
         } else {  
           if (u < x) a=u; else b=u;  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
           if (fu <= fw || w == x) {  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
             v=w;  
             w=u;  #define NINTERVMAX 8
             fv=fw;  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
             fw=fu;  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
           } else if (fu <= fv || v == x || v == w) {  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
             v=u;  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
             fv=fu;  #define MAXN 20000
           }  #define YEARM 12. /**< Number of months per year */
         }  #define AGESUP 130
   }  #define AGEBASE 40
   nrerror("Too many iterations in brent");  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
   *xmin=x;  #ifdef UNIX
   return fx;  #define DIRSEPARATOR '/'
 }  #define CHARSEPARATOR "/"
   #define ODIRSEPARATOR '\\'
 /****************** mnbrak ***********************/  #else
   #define DIRSEPARATOR '\\'
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #define CHARSEPARATOR "\\"
             double (*func)(double))  #define ODIRSEPARATOR '/'
 {  #endif
   double ulim,u,r,q, dum;  
   double fu;  <<<<<<< imach.c
    /* $Id$ */
   *fa=(*func)(*ax);  =======
   *fb=(*func)(*bx);  /* $Id$ */
   if (*fb > *fa) {  >>>>>>> 1.145
     SHFT(dum,*ax,*bx,dum)  /* $State$ */
       SHFT(dum,*fb,*fa,dum)  
       }  <<<<<<< imach.c
   *cx=(*bx)+GOLD*(*bx-*ax);  char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
   *fc=(*func)(*cx);  char fullversion[]="$Revision$ $Date$"; 
   while (*fb > *fc) {  =======
     r=(*bx-*ax)*(*fb-*fc);  char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
     q=(*bx-*cx)*(*fb-*fa);  char fullversion[]="$Revision$ $Date$"; 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  >>>>>>> 1.145
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  char strstart[80];
     ulim=(*bx)+GLIMIT*(*cx-*bx);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
     if ((*bx-u)*(u-*cx) > 0.0) {  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
       fu=(*func)(u);  int nvar=0, nforce=0; /* Number of variables, number of forces */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
       fu=(*func)(u);  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
       if (fu < *fc) {  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
           SHFT(*fb,*fc,fu,(*func)(u))  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
           }  int cptcovprodnoage=0; /**< Number of covariate products without age */   
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  int cptcoveff=0; /* Total number of covariates to vary for printing results */
       u=ulim;  int cptcov=0; /* Working variable */
       fu=(*func)(u);  int npar=NPARMAX;
     } else {  int nlstate=2; /* Number of live states */
       u=(*cx)+GOLD*(*cx-*bx);  int ndeath=1; /* Number of dead states */
       fu=(*func)(u);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     }  int popbased=0;
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)  int *wav; /* Number of waves for this individuual 0 is possible */
       }  int maxwav=0; /* Maxim number of waves */
 }  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
 /*************** linmin ************************/  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
 int ncom;  int mle=1, weightopt=0;
 double *pcom,*xicom;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 double (*nrfunc)(double []);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
    int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 {  double jmean=1; /* Mean space between 2 waves */
   double brent(double ax, double bx, double cx,  double **matprod2(); /* test */
                double (*f)(double), double tol, double *xmin);  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double f1dim(double x);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /*FILE *fic ; */ /* Used in readdata only */
               double *fc, double (*func)(double));  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   int j;  FILE *ficlog, *ficrespow;
   double xx,xmin,bx,ax;  int globpr=0; /* Global variable for printing or not */
   double fx,fb,fa;  double fretone; /* Only one call to likelihood */
    long ipmx=0; /* Number of contributions */
   ncom=n;  double sw; /* Sum of weights */
   pcom=vector(1,n);  char filerespow[FILENAMELENGTH];
   xicom=vector(1,n);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   nrfunc=func;  FILE *ficresilk;
   for (j=1;j<=n;j++) {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     pcom[j]=p[j];  FILE *ficresprobmorprev;
     xicom[j]=xi[j];  FILE *fichtm, *fichtmcov; /* Html File */
   }  FILE *ficreseij;
   ax=0.0;  char filerese[FILENAMELENGTH];
   xx=1.0;  FILE *ficresstdeij;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  char fileresstde[FILENAMELENGTH];
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  FILE *ficrescveij;
 #ifdef DEBUG  char filerescve[FILENAMELENGTH];
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  FILE  *ficresvij;
 #endif  char fileresv[FILENAMELENGTH];
   for (j=1;j<=n;j++) {  FILE  *ficresvpl;
     xi[j] *= xmin;  char fileresvpl[FILENAMELENGTH];
     p[j] += xi[j];  char title[MAXLINE];
   }  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   free_vector(xicom,1,n);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   free_vector(pcom,1,n);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 }  char command[FILENAMELENGTH];
   int  outcmd=0;
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
             double (*func)(double []))  
 {  char filelog[FILENAMELENGTH]; /* Log file */
   void linmin(double p[], double xi[], int n, double *fret,  char filerest[FILENAMELENGTH];
               double (*func)(double []));  char fileregp[FILENAMELENGTH];
   int i,ibig,j;  char popfile[FILENAMELENGTH];
   double del,t,*pt,*ptt,*xit;  
   double fp,fptt;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   double *xits;  
   pt=vector(1,n);  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   ptt=vector(1,n);  struct timezone tzp;
   xit=vector(1,n);  extern int gettimeofday();
   xits=vector(1,n);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   *fret=(*func)(p);  long time_value;
   for (j=1;j<=n;j++) pt[j]=p[j];  extern long time();
   for (*iter=1;;++(*iter)) {  char strcurr[80], strfor[80];
     fp=(*fret);  
     ibig=0;  char *endptr;
     del=0.0;  long lval;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  double dval;
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  #define NR_END 1
     printf("\n");  #define FREE_ARG char*
     for (i=1;i<=n;i++) {  #define FTOL 1.0e-10
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  #define NRANSI 
 #ifdef DEBUG  #define ITMAX 200 
       printf("fret=%lf \n",*fret);  
 #endif  #define TOL 2.0e-4 
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  #define CGOLD 0.3819660 
       if (fabs(fptt-(*fret)) > del) {  #define ZEPS 1.0e-10 
         del=fabs(fptt-(*fret));  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
         ibig=i;  
       }  #define GOLD 1.618034 
 #ifdef DEBUG  #define GLIMIT 100.0 
       printf("%d %.12e",i,(*fret));  #define TINY 1.0e-20 
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  static double maxarg1,maxarg2;
         printf(" x(%d)=%.12e",j,xit[j]);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       }  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       for(j=1;j<=n;j++)    
         printf(" p=%.12e",p[j]);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       printf("\n");  #define rint(a) floor(a+0.5)
 #endif  
     }  static double sqrarg;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #ifdef DEBUG  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       int k[2],l;  int agegomp= AGEGOMP;
       k[0]=1;  
       k[1]=-1;  int imx; 
       printf("Max: %.12e",(*func)(p));  int stepm=1;
       for (j=1;j<=n;j++)  /* Stepm, step in month: minimum step interpolation*/
         printf(" %.12e",p[j]);  
       printf("\n");  int estepm;
       for(l=0;l<=1;l++) {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  int m,nb;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  long *num;
         }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       }  double **pmmij, ***probs;
 #endif  double *ageexmed,*agecens;
   double dateintmean=0;
   
       free_vector(xit,1,n);  double *weight;
       free_vector(xits,1,n);  int **s; /* Status */
       free_vector(ptt,1,n);  double *agedc;
       free_vector(pt,1,n);  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
       return;                    * covar=matrix(0,NCOVMAX,1,n); 
     }                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  double  idx; 
     for (j=1;j<=n;j++) {  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
       ptt[j]=2.0*p[j]-pt[j];  int *Ndum; /** Freq of modality (tricode */
       xit[j]=p[j]-pt[j];  int **codtab; /**< codtab=imatrix(1,100,1,10); */
       pt[j]=p[j];  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
     }  double *lsurv, *lpop, *tpop;
     fptt=(*func)(ptt);  
     if (fptt < fp) {  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  double ftolhess; /**< Tolerance for computing hessian */
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  /**************** split *************************/
         for (j=1;j<=n;j++) {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
           xi[j][ibig]=xi[j][n];  {
           xi[j][n]=xit[j];    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
         }       the name of the file (name), its extension only (ext) and its first part of the name (finame)
 #ifdef DEBUG    */ 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    char  *ss;                            /* pointer */
         for(j=1;j<=n;j++)    int   l1, l2;                         /* length counters */
           printf(" %.12e",xit[j]);  
         printf("\n");    l1 = strlen(path );                   /* length of path */
 #endif    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     }    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   }      strcpy( name, path );               /* we got the fullname name because no directory */
 }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 /**** Prevalence limit ****************/      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 {        return( GLOCK_ERROR_GETCWD );
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      }
      matrix by transitions matrix until convergence is reached */      /* got dirc from getcwd*/
       printf(" DIRC = %s \n",dirc);
   int i, ii,j,k;    } else {                              /* strip direcotry from path */
   double min, max, maxmin, maxmax,sumnew=0.;      ss++;                               /* after this, the filename */
   double **matprod2();      l2 = strlen( ss );                  /* length of filename */
   double **out, cov[NCOVMAX], **pmij();      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   double **newm;      strcpy( name, ss );         /* save file name */
   double agefin, delaymax=50 ; /* Max number of years to converge */      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
   for (ii=1;ii<=nlstate+ndeath;ii++)      printf(" DIRC2 = %s \n",dirc);
     for (j=1;j<=nlstate+ndeath;j++){    }
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    /* We add a separator at the end of dirc if not exists */
     }    l1 = strlen( dirc );                  /* length of directory */
     if( dirc[l1-1] != DIRSEPARATOR ){
    cov[1]=1.;      dirc[l1] =  DIRSEPARATOR;
        dirc[l1+1] = 0; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      printf(" DIRC3 = %s \n",dirc);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    }
     newm=savm;    ss = strrchr( name, '.' );            /* find last / */
     /* Covariates have to be included here again */    if (ss >0){
      cov[2]=agefin;      ss++;
        strcpy(ext,ss);                     /* save extension */
       for (k=1; k<=cptcovn;k++) {      l1= strlen( name);
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      l2= strlen(ss)+1;
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/      strncpy( finame, name, l1-l2);
       }      finame[l1-l2]= 0;
       for (k=1; k<=cptcovage;k++)    }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)    return( 0 );                          /* we're done */
         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]);*/  
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  /******************************************/
   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  void replace_back_to_slash(char *s, char*t)
   {
     savm=oldm;    int i;
     oldm=newm;    int lg=0;
     maxmax=0.;    i=0;
     for(j=1;j<=nlstate;j++){    lg=strlen(t);
       min=1.;    for(i=0; i<= lg; i++) {
       max=0.;      (s[i] = t[i]);
       for(i=1; i<=nlstate; i++) {      if (t[i]== '\\') s[i]='/';
         sumnew=0;    }
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  }
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  char *trimbb(char *out, char *in)
         min=FMIN(min,prlim[i][j]);  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
       }    char *s;
       maxmin=max-min;    s=out;
       maxmax=FMAX(maxmax,maxmin);    while (*in != '\0'){
     }      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
     if(maxmax < ftolpl){        in++;
       return prlim;      }
     }      *out++ = *in++;
   }    }
 }    *out='\0';
     return s;
 /*************** transition probabilities ***************/  }
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  char *cutl(char *blocc, char *alocc, char *in, char occ)
 {  {
   double s1, s2;    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
   /*double t34;*/       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   int i,j,j1, nc, ii, jj;       gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns blocc
     for(i=1; i<= nlstate; i++){    */
     for(j=1; j<i;j++){    char *s, *t, *bl;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    t=in;s=in;
         /*s2 += param[i][j][nc]*cov[nc];*/    while ((*in != occ) && (*in != '\0')){
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      *alocc++ = *in++;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    }
       }    if( *in == occ){
       ps[i][j]=s2;      *(alocc)='\0';
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      s=++in;
     }    }
     for(j=i+1; j<=nlstate+ndeath;j++){   
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    if (s == t) {/* occ not found */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      *(alocc-(in-s))='\0';
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      in=s;
       }    }
       ps[i][j]=s2;    while ( *in != '\0'){
     }      *blocc++ = *in++;
   }    }
     /*ps[3][2]=1;*/  
     *blocc='\0';
   for(i=1; i<= nlstate; i++){    return t;
      s1=0;  }
     for(j=1; j<i; j++)  char *cutv(char *blocc, char *alocc, char *in, char occ)
       s1+=exp(ps[i][j]);  {
     for(j=i+1; j<=nlstate+ndeath; j++)    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
       s1+=exp(ps[i][j]);       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     ps[i][i]=1./(s1+1.);       gives blocc="abcdef2ghi" and alocc="j".
     for(j=1; j<i; j++)       If occ is not found blocc is null and alocc is equal to in. Returns alocc
       ps[i][j]= exp(ps[i][j])*ps[i][i];    */
     for(j=i+1; j<=nlstate+ndeath; j++)    char *s, *t;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    t=in;s=in;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    while (*in != '\0'){
   } /* end i */      while( *in == occ){
         *blocc++ = *in++;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        s=in;
     for(jj=1; jj<= nlstate+ndeath; jj++){      }
       ps[ii][jj]=0;      *blocc++ = *in++;
       ps[ii][ii]=1;    }
     }    if (s == t) /* occ not found */
   }      *(blocc-(in-s))='\0';
     else
       *(blocc-(in-s)-1)='\0';
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    in=s;
     for(jj=1; jj<= nlstate+ndeath; jj++){    while ( *in != '\0'){
      printf("%lf ",ps[ii][jj]);      *alocc++ = *in++;
    }    }
     printf("\n ");  
     }    *alocc='\0';
     printf("\n ");printf("%lf ",cov[2]);*/    return s;
 /*  }
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  
   goto end;*/  int nbocc(char *s, char occ)
     return ps;  {
 }    int i,j=0;
     int lg=20;
 /**************** Product of 2 matrices ******************/    i=0;
     lg=strlen(s);
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    for(i=0; i<= lg; i++) {
 {    if  (s[i] == occ ) j++;
   /* 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(...) */    return j;
   /* 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 */  /* void cutv(char *u,char *v, char*t, char occ) */
   long i, j, k;  /* { */
   for(i=nrl; i<= nrh; i++)  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
     for(k=ncolol; k<=ncoloh; k++)  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  /*      gives u="abcdef2ghi" and v="j" *\/ */
         out[i][k] +=in[i][j]*b[j][k];  /*   int i,lg,j,p=0; */
   /*   i=0; */
   return out;  /*   lg=strlen(t); */
 }  /*   for(j=0; j<=lg-1; j++) { */
   /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   /*   } */
 /************* Higher Matrix Product ***************/  
   /*   for(j=0; j<p; j++) { */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  /*     (u[j] = t[j]); */
 {  /*   } */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  /*      u[p]='\0'; */
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  /*    for(j=0; j<= lg; j++) { */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
      (typically every 2 years instead of every month which is too big).  /*   } */
      Model is determined by parameters x and covariates have to be  /* } */
      included manually here.  
   /********************** nrerror ********************/
      */  
   void nrerror(char error_text[])
   int i, j, d, h, k;  {
   double **out, cov[NCOVMAX];    fprintf(stderr,"ERREUR ...\n");
   double **newm;    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
   /* Hstepm could be zero and should return the unit matrix */  }
   for (i=1;i<=nlstate+ndeath;i++)  /*********************** vector *******************/
     for (j=1;j<=nlstate+ndeath;j++){  double *vector(int nl, int nh)
       oldm[i][j]=(i==j ? 1.0 : 0.0);  {
       po[i][j][0]=(i==j ? 1.0 : 0.0);    double *v;
     }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    if (!v) nrerror("allocation failure in vector");
   for(h=1; h <=nhstepm; h++){    return v-nl+NR_END;
     for(d=1; d <=hstepm; d++){  }
       newm=savm;  
       /* Covariates have to be included here again */  /************************ free vector ******************/
       cov[1]=1.;  void free_vector(double*v, int nl, int nh)
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  {
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    free((FREE_ARG)(v+nl-NR_END));
       for (k=1; k<=cptcovage;k++)  }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  /************************ivector *******************************/
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  int *ivector(long nl,long nh)
   {
     int *v;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    if (!v) nrerror("allocation failure in ivector");
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    return v-nl+NR_END;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  }
       savm=oldm;  
       oldm=newm;  /******************free ivector **************************/
     }  void free_ivector(int *v, long nl, long nh)
     for(i=1; i<=nlstate+ndeath; i++)  {
       for(j=1;j<=nlstate+ndeath;j++) {    free((FREE_ARG)(v+nl-NR_END));
         po[i][j][h]=newm[i][j];  }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  /************************lvector *******************************/
       }  long *lvector(long nl,long nh)
   } /* end h */  {
   return po;    long *v;
 }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
 /*************** log-likelihood *************/  }
 double func( double *x)  
 {  /******************free lvector **************************/
   int i, ii, j, k, mi, d, kk;  void free_lvector(long *v, long nl, long nh)
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  {
   double **out;    free((FREE_ARG)(v+nl-NR_END));
   double sw; /* Sum of weights */  }
   double lli; /* Individual log likelihood */  
   long ipmx;  /******************* imatrix *******************************/
   /*extern weight */  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   /* We are differentiating ll according to initial status */       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  { 
   /*for(i=1;i<imx;i++)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     printf(" %d\n",s[4][i]);    int **m; 
   */    
   cov[1]=1.;    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    m += NR_END; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    m -= nrl; 
     for(mi=1; mi<= wav[i]-1; mi++){    
       for (ii=1;ii<=nlstate+ndeath;ii++)    
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    /* allocate rows and set pointers to them */ 
       for(d=0; d<dh[mi][i]; d++){    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         newm=savm;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    m[nrl] += NR_END; 
         for (kk=1; kk<=cptcovage;kk++) {    m[nrl] -= ncl; 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    
         }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
            
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    /* return pointer to array of pointers to rows */ 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    return m; 
         savm=oldm;  } 
         oldm=newm;  
          /****************** free_imatrix *************************/
          void free_imatrix(m,nrl,nrh,ncl,nch)
       } /* end mult */        int **m;
              long nch,ncl,nrh,nrl; 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);       /* free an int matrix allocated by imatrix() */ 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  { 
       ipmx +=1;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       sw += weight[i];    free((FREE_ARG) (m+nrl-NR_END)); 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  } 
     } /* end of wave */  
   } /* end of individual */  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  {
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    double **m;
   return -l;  
 }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
 /*********** Maximum Likelihood Estimation ***************/    m -= nrl;
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   int i,j, iter;    m[nrl] += NR_END;
   double **xi,*delti;    m[nrl] -= ncl;
   double fret;  
   xi=matrix(1,npar,1,npar);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for (i=1;i<=npar;i++)    return m;
     for (j=1;j<=npar;j++)    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
       xi[i][j]=(i==j ? 1.0 : 0.0);  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   printf("Powell\n");  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
   powell(p,xi,npar,ftol,&iter,&fret,func);     */
   }
    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 matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 }  {
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
 /**** Computes Hessian and covariance matrix ***/    free((FREE_ARG)(m+nrl-NR_END));
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  }
 {  
   double  **a,**y,*x,pd;  /******************* ma3x *******************************/
   double **hess;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   int i, j,jk;  {
   int *indx;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   void lubksb(double **a, int npar, int *indx, double b[]) ;    if (!m) nrerror("allocation failure 1 in matrix()");
   void ludcmp(double **a, int npar, int *indx, double *d) ;    m += NR_END;
     m -= nrl;
   hess=matrix(1,npar,1,npar);  
     m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   printf("\nCalculation of the hessian matrix. Wait...\n");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for (i=1;i<=npar;i++){    m[nrl] += NR_END;
     printf("%d",i);fflush(stdout);    m[nrl] -= ncl;
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     /*printf(" %lf ",hess[i][i]);*/  
   }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
      if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   for (i=1;i<=npar;i++) {    m[nrl][ncl] += NR_END;
     for (j=1;j<=npar;j++)  {    m[nrl][ncl] -= nll;
       if (j>i) {    for (j=ncl+1; j<=nch; j++) 
         printf(".%d%d",i,j);fflush(stdout);      m[nrl][j]=m[nrl][j-1]+nlay;
         hess[i][j]=hessij(p,delti,i,j);    
         hess[j][i]=hess[i][j];        for (i=nrl+1; i<=nrh; i++) {
         /*printf(" %lf ",hess[i][j]);*/      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       }      for (j=ncl+1; j<=nch; j++) 
     }        m[i][j]=m[i][j-1]+nlay;
   }    }
   printf("\n");    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
      */
   a=matrix(1,npar,1,npar);  }
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);  /*************************free ma3x ************************/
   indx=ivector(1,npar);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   for (i=1;i<=npar;i++)  {
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   ludcmp(a,npar,indx,&pd);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
   for (j=1;j<=npar;j++) {  }
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  /*************** function subdirf ***********/
     lubksb(a,npar,indx,x);  char *subdirf(char fileres[])
     for (i=1;i<=npar;i++){  {
       matcov[i][j]=x[i];    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
   }    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
   printf("\n#Hessian matrix#\n");    return tmpout;
   for (i=1;i<=npar;i++) {  }
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);  /*************** function subdirf2 ***********/
     }  char *subdirf2(char fileres[], char *preop)
     printf("\n");  {
   }    
     /* Caution optionfilefiname is hidden */
   /* Recompute Inverse */    strcpy(tmpout,optionfilefiname);
   for (i=1;i<=npar;i++)    strcat(tmpout,"/");
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    strcat(tmpout,preop);
   ludcmp(a,npar,indx,&pd);    strcat(tmpout,fileres);
     return tmpout;
   /*  printf("\n#Hessian matrix recomputed#\n");  }
   
   for (j=1;j<=npar;j++) {  /*************** function subdirf3 ***********/
     for (i=1;i<=npar;i++) x[i]=0;  char *subdirf3(char fileres[], char *preop, char *preop2)
     x[j]=1;  {
     lubksb(a,npar,indx,x);    
     for (i=1;i<=npar;i++){    /* Caution optionfilefiname is hidden */
       y[i][j]=x[i];    strcpy(tmpout,optionfilefiname);
       printf("%.3e ",y[i][j]);    strcat(tmpout,"/");
     }    strcat(tmpout,preop);
     printf("\n");    strcat(tmpout,preop2);
   }    strcat(tmpout,fileres);
   */    return tmpout;
   }
   free_matrix(a,1,npar,1,npar);  
   free_matrix(y,1,npar,1,npar);  /***************** f1dim *************************/
   free_vector(x,1,npar);  extern int ncom; 
   free_ivector(indx,1,npar);  extern double *pcom,*xicom;
   free_matrix(hess,1,npar,1,npar);  extern double (*nrfunc)(double []); 
    
   double f1dim(double x) 
 }  { 
     int j; 
 /*************** hessian matrix ****************/    double f;
 double hessii( double x[], double delta, int theta, double delti[])    double *xt; 
 {   
   int i;    xt=vector(1,ncom); 
   int l=1, lmax=20;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   double k1,k2;    f=(*nrfunc)(xt); 
   double p2[NPARMAX+1];    free_vector(xt,1,ncom); 
   double res;    return f; 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  } 
   double fx;  
   int k=0,kmax=10;  /*****************brent *************************/
   double l1;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
   fx=func(x);    int iter; 
   for (i=1;i<=npar;i++) p2[i]=x[i];    double a,b,d,etemp;
   for(l=0 ; l <=lmax; l++){    double fu,fv,fw,fx;
     l1=pow(10,l);    double ftemp;
     delts=delt;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     for(k=1 ; k <kmax; k=k+1){    double e=0.0; 
       delt = delta*(l1*k);   
       p2[theta]=x[theta] +delt;    a=(ax < cx ? ax : cx); 
       k1=func(p2)-fx;    b=(ax > cx ? ax : cx); 
       p2[theta]=x[theta]-delt;    x=w=v=bx; 
       k2=func(p2)-fx;    fw=fv=fx=(*f)(x); 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    for (iter=1;iter<=ITMAX;iter++) { 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      xm=0.5*(a+b); 
            tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 #ifdef DEBUG      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       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);      printf(".");fflush(stdout);
 #endif      fprintf(ficlog,".");fflush(ficlog);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  #ifdef DEBUG
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      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);
         k=kmax;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  #endif
         k=kmax; l=lmax*10.;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       }        *xmin=x; 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        return fx; 
         delts=delt;      } 
       }      ftemp=fu;
     }      if (fabs(e) > tol1) { 
   }        r=(x-w)*(fx-fv); 
   delti[theta]=delts;        q=(x-v)*(fx-fw); 
   return res;        p=(x-v)*q-(x-w)*r; 
          q=2.0*(q-r); 
 }        if (q > 0.0) p = -p; 
         q=fabs(q); 
 double hessij( double x[], double delti[], int thetai,int thetaj)        etemp=e; 
 {        e=d; 
   int i;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   int l=1, l1, lmax=20;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double k1,k2,k3,k4,res,fx;        else { 
   double p2[NPARMAX+1];          d=p/q; 
   int k;          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
   fx=func(x);            d=SIGN(tol1,xm-x); 
   for (k=1; k<=2; k++) {        } 
     for (i=1;i<=npar;i++) p2[i]=x[i];      } else { 
     p2[thetai]=x[thetai]+delti[thetai]/k;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      } 
     k1=func(p2)-fx;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
        fu=(*f)(u); 
     p2[thetai]=x[thetai]+delti[thetai]/k;      if (fu <= fx) { 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        if (u >= x) a=x; else b=x; 
     k2=func(p2)-fx;        SHFT(v,w,x,u) 
            SHFT(fv,fw,fx,fu) 
     p2[thetai]=x[thetai]-delti[thetai]/k;          } else { 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            if (u < x) a=u; else b=u; 
     k3=func(p2)-fx;            if (fu <= fw || w == x) { 
                v=w; 
     p2[thetai]=x[thetai]-delti[thetai]/k;              w=u; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;              fv=fw; 
     k4=func(p2)-fx;              fw=fu; 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */            } else if (fu <= fv || v == x || v == w) { 
 #ifdef DEBUG              v=u; 
     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);              fv=fu; 
 #endif            } 
   }          } 
   return res;    } 
 }    nrerror("Too many iterations in brent"); 
     *xmin=x; 
 /************** Inverse of matrix **************/    return fx; 
 void ludcmp(double **a, int n, int *indx, double *d)  } 
 {  
   int i,imax,j,k;  /****************** mnbrak ***********************/
   double big,dum,sum,temp;  
   double *vv;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
                double (*func)(double)) 
   vv=vector(1,n);  { 
   *d=1.0;    double ulim,u,r,q, dum;
   for (i=1;i<=n;i++) {    double fu; 
     big=0.0;   
     for (j=1;j<=n;j++)    *fa=(*func)(*ax); 
       if ((temp=fabs(a[i][j])) > big) big=temp;    *fb=(*func)(*bx); 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    if (*fb > *fa) { 
     vv[i]=1.0/big;      SHFT(dum,*ax,*bx,dum) 
   }        SHFT(dum,*fb,*fa,dum) 
   for (j=1;j<=n;j++) {        } 
     for (i=1;i<j;i++) {    *cx=(*bx)+GOLD*(*bx-*ax); 
       sum=a[i][j];    *fc=(*func)(*cx); 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    while (*fb > *fc) { 
       a[i][j]=sum;      r=(*bx-*ax)*(*fb-*fc); 
     }      q=(*bx-*cx)*(*fb-*fa); 
     big=0.0;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     for (i=j;i<=n;i++) {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       sum=a[i][j];      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       for (k=1;k<j;k++)      if ((*bx-u)*(u-*cx) > 0.0) { 
         sum -= a[i][k]*a[k][j];        fu=(*func)(u); 
       a[i][j]=sum;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       if ( (dum=vv[i]*fabs(sum)) >= big) {        fu=(*func)(u); 
         big=dum;        if (fu < *fc) { 
         imax=i;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       }            SHFT(*fb,*fc,fu,(*func)(u)) 
     }            } 
     if (j != imax) {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       for (k=1;k<=n;k++) {        u=ulim; 
         dum=a[imax][k];        fu=(*func)(u); 
         a[imax][k]=a[j][k];      } else { 
         a[j][k]=dum;        u=(*cx)+GOLD*(*cx-*bx); 
       }        fu=(*func)(u); 
       *d = -(*d);      } 
       vv[imax]=vv[j];      SHFT(*ax,*bx,*cx,u) 
     }        SHFT(*fa,*fb,*fc,fu) 
     indx[j]=imax;        } 
     if (a[j][j] == 0.0) a[j][j]=TINY;  } 
     if (j != n) {  
       dum=1.0/(a[j][j]);  /*************** linmin ************************/
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }  int ncom; 
   }  double *pcom,*xicom;
   free_vector(vv,1,n);  /* Doesn't work */  double (*nrfunc)(double []); 
 ;   
 }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   { 
 void lubksb(double **a, int n, int *indx, double b[])    double brent(double ax, double bx, double cx, 
 {                 double (*f)(double), double tol, double *xmin); 
   int i,ii=0,ip,j;    double f1dim(double x); 
   double sum;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                  double *fc, double (*func)(double)); 
   for (i=1;i<=n;i++) {    int j; 
     ip=indx[i];    double xx,xmin,bx,ax; 
     sum=b[ip];    double fx,fb,fa;
     b[ip]=b[i];   
     if (ii)    ncom=n; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    pcom=vector(1,n); 
     else if (sum) ii=i;    xicom=vector(1,n); 
     b[i]=sum;    nrfunc=func; 
   }    for (j=1;j<=n;j++) { 
   for (i=n;i>=1;i--) {      pcom[j]=p[j]; 
     sum=b[i];      xicom[j]=xi[j]; 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    } 
     b[i]=sum/a[i][i];    ax=0.0; 
   }    xx=1.0; 
 }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 /************ Frequencies ********************/  #ifdef DEBUG
 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)    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 {  /* Some frequencies */    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
    #endif
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    for (j=1;j<=n;j++) { 
   double ***freq; /* Frequencies */      xi[j] *= xmin; 
   double *pp;      p[j] += xi[j]; 
   double pos, k2, dateintsum=0,k2cpt=0;    } 
   FILE *ficresp;    free_vector(xicom,1,n); 
   char fileresp[FILENAMELENGTH];    free_vector(pcom,1,n); 
   } 
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  char *asc_diff_time(long time_sec, char ascdiff[])
   strcpy(fileresp,"p");  {
   strcat(fileresp,fileres);    long sec_left, days, hours, minutes;
   if((ficresp=fopen(fileresp,"w"))==NULL) {    days = (time_sec) / (60*60*24);
     printf("Problem with prevalence resultfile: %s\n", fileresp);    sec_left = (time_sec) % (60*60*24);
     exit(0);    hours = (sec_left) / (60*60) ;
   }    sec_left = (sec_left) %(60*60);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    minutes = (sec_left) /60;
   j1=0;    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
   j=cptcoveff;    return ascdiff;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  }
   
   for(k1=1; k1<=j;k1++){  /*************** powell ************************/
    for(i1=1; i1<=ncodemax[k1];i1++){  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
        j1++;              double (*func)(double [])) 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  { 
          scanf("%d", i);*/    void linmin(double p[], double xi[], int n, double *fret, 
         for (i=-1; i<=nlstate+ndeath; i++)                  double (*func)(double [])); 
          for (jk=-1; jk<=nlstate+ndeath; jk++)      int i,ibig,j; 
            for(m=agemin; m <= agemax+3; m++)    double del,t,*pt,*ptt,*xit;
              freq[i][jk][m]=0;    double fp,fptt;
     double *xits;
         dateintsum=0;    int niterf, itmp;
         k2cpt=0;  
        for (i=1; i<=imx; i++) {    pt=vector(1,n); 
          bool=1;    ptt=vector(1,n); 
          if  (cptcovn>0) {    xit=vector(1,n); 
            for (z1=1; z1<=cptcoveff; z1++)    xits=vector(1,n); 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    *fret=(*func)(p); 
                bool=0;    for (j=1;j<=n;j++) pt[j]=p[j]; 
          }    for (*iter=1;;++(*iter)) { 
          if (bool==1) {      fp=(*fret); 
            for(m=firstpass; m<=lastpass; m++){      ibig=0; 
              k2=anint[m][i]+(mint[m][i]/12.);      del=0.0; 
              if ((k2>=dateprev1) && (k2<=dateprev2)) {      last_time=curr_time;
                if(agev[m][i]==0) agev[m][i]=agemax+1;      (void) gettimeofday(&curr_time,&tzp);
                if(agev[m][i]==1) agev[m][i]=agemax+2;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {     for (i=1;i<=n;i++) {
                  dateintsum=dateintsum+k2;        printf(" %d %.12f",i, p[i]);
                  k2cpt++;        fprintf(ficlog," %d %.12lf",i, p[i]);
                }        fprintf(ficrespow," %.12lf", p[i]);
       }
              }      printf("\n");
            }      fprintf(ficlog,"\n");
          }      fprintf(ficrespow,"\n");fflush(ficrespow);
        }      if(*iter <=3){
         if  (cptcovn>0) {        tm = *localtime(&curr_time.tv_sec);
          fprintf(ficresp, "\n#********** Variable ");        strcpy(strcurr,asctime(&tm));
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  /*       asctime_r(&tm,strcurr); */
        fprintf(ficresp, "**********\n#");        forecast_time=curr_time; 
         }        itmp = strlen(strcurr);
        for(i=1; i<=nlstate;i++)        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          strcurr[itmp-1]='\0';
        fprintf(ficresp, "\n");        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   for(i=(int)agemin; i <= (int)agemax+3; i++){        for(niterf=10;niterf<=30;niterf+=10){
     if(i==(int)agemax+3)          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       printf("Total");          tmf = *localtime(&forecast_time.tv_sec);
     else  /*      asctime_r(&tmf,strfor); */
       printf("Age %d", i);          strcpy(strfor,asctime(&tmf));
     for(jk=1; jk <=nlstate ; jk++){          itmp = strlen(strfor);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          if(strfor[itmp-1]=='\n')
         pp[jk] += freq[jk][m][i];          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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     for(jk=1; jk <=nlstate ; 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(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       for(m=-1, pos=0; m <=0 ; m++)        }
         pos += freq[jk][m][i];      }
       if(pp[jk]>=1.e-10)      for (i=1;i<=n;i++) { 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       else        fptt=(*fret); 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  #ifdef DEBUG
     }        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
      for(jk=1; jk <=nlstate ; jk++){  #endif
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        printf("%d",i);fflush(stdout);
         pp[jk] += freq[jk][m][i];        fprintf(ficlog,"%d",i);fflush(ficlog);
      }        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
     for(jk=1,pos=0; jk <=nlstate ; jk++)          del=fabs(fptt-(*fret)); 
       pos += pp[jk];          ibig=i; 
     for(jk=1; jk <=nlstate ; jk++){        } 
       if(pos>=1.e-5)  #ifdef DEBUG
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        printf("%d %.12e",i,(*fret));
       else        fprintf(ficlog,"%d %.12e",i,(*fret));
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        for (j=1;j<=n;j++) {
       if( i <= (int) agemax){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         if(pos>=1.e-5){          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
           probs[i][jk][j1]= pp[jk]/pos;        }
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        for(j=1;j<=n;j++) {
         }          printf(" p=%.12e",p[j]);
       else          fprintf(ficlog," p=%.12e",p[j]);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        }
       }        printf("\n");
     }        fprintf(ficlog,"\n");
     for(jk=-1; jk <=nlstate+ndeath; jk++)  #endif
       for(m=-1; m <=nlstate+ndeath; m++)      } 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     if(i <= (int) agemax)  #ifdef DEBUG
       fprintf(ficresp,"\n");        int k[2],l;
     printf("\n");        k[0]=1;
     }        k[1]=-1;
     }        printf("Max: %.12e",(*func)(p));
  }        fprintf(ficlog,"Max: %.12e",(*func)(p));
   dateintmean=dateintsum/k2cpt;        for (j=1;j<=n;j++) {
            printf(" %.12e",p[j]);
   fclose(ficresp);          fprintf(ficlog," %.12e",p[j]);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        }
   free_vector(pp,1,nlstate);        printf("\n");
         fprintf(ficlog,"\n");
   /* End of Freq */        for(l=0;l<=1;l++) {
 }          for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 /************ Prevalence ********************/            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 {  /* Some frequencies */          }
            printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double ***freq; /* Frequencies */        }
   double *pp;  #endif
   double pos, k2;  
   
   pp=vector(1,nlstate);        free_vector(xit,1,n); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        free_vector(xits,1,n); 
          free_vector(ptt,1,n); 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        free_vector(pt,1,n); 
   j1=0;        return; 
        } 
   j=cptcoveff;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for (j=1;j<=n;j++) { 
          ptt[j]=2.0*p[j]-pt[j]; 
  for(k1=1; k1<=j;k1++){        xit[j]=p[j]-pt[j]; 
     for(i1=1; i1<=ncodemax[k1];i1++){        pt[j]=p[j]; 
       j1++;      } 
        fptt=(*func)(ptt); 
       for (i=-1; i<=nlstate+ndeath; i++)        if (fptt < fp) { 
         for (jk=-1; jk<=nlstate+ndeath; jk++)          t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
           for(m=agemin; m <= agemax+3; m++)        if (t < 0.0) { 
             freq[i][jk][m]=0;          linmin(p,xit,n,fret,func); 
                for (j=1;j<=n;j++) { 
       for (i=1; i<=imx; i++) {            xi[j][ibig]=xi[j][n]; 
         bool=1;            xi[j][n]=xit[j]; 
         if  (cptcovn>0) {          }
           for (z1=1; z1<=cptcoveff; z1++)  #ifdef DEBUG
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
               bool=0;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         }          for(j=1;j<=n;j++){
         if (bool==1) {            printf(" %.12e",xit[j]);
           for(m=firstpass; m<=lastpass; m++){            fprintf(ficlog," %.12e",xit[j]);
             k2=anint[m][i]+(mint[m][i]/12.);          }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          printf("\n");
               if(agev[m][i]==0) agev[m][i]=agemax+1;          fprintf(ficlog,"\n");
               if(agev[m][i]==1) agev[m][i]=agemax+2;  #endif
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        }
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];        } 
             }    } 
           }  } 
         }  
       }  /**** Prevalence limit (stable or period prevalence)  ****************/
        
         for(i=(int)agemin; i <= (int)agemax+3; i++){  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
           for(jk=1; jk <=nlstate ; jk++){  {
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
               pp[jk] += freq[jk][m][i];       matrix by transitions matrix until convergence is reached */
           }  
           for(jk=1; jk <=nlstate ; jk++){    int i, ii,j,k;
             for(m=-1, pos=0; m <=0 ; m++)    double min, max, maxmin, maxmax,sumnew=0.;
             pos += freq[jk][m][i];    /* double **matprod2(); */ /* test */
         }    double **out, cov[NCOVMAX+1], **pmij();
            double **newm;
          for(jk=1; jk <=nlstate ; jk++){    double agefin, delaymax=50 ; /* Max number of years to converge */
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
              pp[jk] += freq[jk][m][i];    for (ii=1;ii<=nlstate+ndeath;ii++)
          }      for (j=1;j<=nlstate+ndeath;j++){
                  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      }
   
          for(jk=1; jk <=nlstate ; jk++){               cov[1]=1.;
            if( i <= (int) agemax){   
              if(pos>=1.e-5){   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                probs[i][jk][j1]= pp[jk]/pos;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
              }      newm=savm;
            }      /* Covariates have to be included here again */
          }      cov[2]=agefin;
                
         }      for (k=1; k<=cptcovn;k++) {
     }        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   }        /*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]]);*/
        }
        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
   free_vector(pp,1,nlstate);      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
        
 }  /* End of Freq */      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
 /************* Waves Concatenation ***************/      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      /* 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 */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      
      Death is a valid wave (if date is known).      savm=oldm;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      oldm=newm;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      maxmax=0.;
      and mw[mi+1][i]. dh depends on stepm.      for(j=1;j<=nlstate;j++){
      */        min=1.;
         max=0.;
   int i, mi, m;        for(i=1; i<=nlstate; i++) {
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          sumnew=0;
      double sum=0., jmean=0.;*/          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           prlim[i][j]= newm[i][j]/(1-sumnew);
   int j, k=0,jk, ju, jl;          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
   double sum=0.;          max=FMAX(max,prlim[i][j]);
   jmin=1e+5;          min=FMIN(min,prlim[i][j]);
   jmax=-1;        }
   jmean=0.;        maxmin=max-min;
   for(i=1; i<=imx; i++){        maxmax=FMAX(maxmax,maxmin);
     mi=0;      }
     m=firstpass;      if(maxmax < ftolpl){
     while(s[m][i] <= nlstate){        return prlim;
       if(s[m][i]>=1)      }
         mw[++mi][i]=m;    }
       if(m >=lastpass)  }
         break;  
       else  /*************** transition probabilities ***************/ 
         m++;  
     }/* end while */  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     if (s[m][i] > nlstate){  {
       mi++;     /* Death is another wave */    /* According to parameters values stored in x and the covariate's values stored in cov,
       /* if(mi==0)  never been interviewed correctly before death */       computes the probability to be observed in state j being in state i by appying the
          /* Only death is a correct wave */       model to the ncovmodel covariates (including constant and age).
       mw[mi][i]=m;       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
     }       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
        ncth covariate in the global vector x is given by the formula:
     wav[i]=mi;       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
     if(mi==0)       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
   }       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
        Outputs ps[i][j] the probability to be observed in j being in j according to
   for(i=1; i<=imx; i++){       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     for(mi=1; mi<wav[i];mi++){    */
       if (stepm <=0)    double s1, lnpijopii;
         dh[mi][i]=1;    /*double t34;*/
       else{    int i,j,j1, nc, ii, jj;
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {      for(i=1; i<= nlstate; i++){
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        for(j=1; j<i;j++){
           if(j==0) j=1;  /* Survives at least one month after exam */          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           k=k+1;            /*lnpijopii += param[i][j][nc]*cov[nc];*/
           if (j >= jmax) jmax=j;            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
           if (j <= jmin) jmin=j;  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
           sum=sum+j;          }
           /* if (j<10) printf("j=%d num=%d ",j,i); */          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
           }  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         }        }
         else{        for(j=i+1; j<=nlstate+ndeath;j++){
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           k=k+1;            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
           if (j >= jmax) jmax=j;            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
           else if (j <= jmin)jmin=j;  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          }
           sum=sum+j;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         }        }
         jk= j/stepm;      }
         jl= j -jk*stepm;      
         ju= j -(jk+1)*stepm;      for(i=1; i<= nlstate; i++){
         if(jl <= -ju)        s1=0;
           dh[mi][i]=jk;        for(j=1; j<i; j++){
         else          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           dh[mi][i]=jk+1;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         if(dh[mi][i]==0)        }
           dh[mi][i]=1; /* At least one step */        for(j=i+1; j<=nlstate+ndeath; j++){
       }          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     }          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   }        }
   jmean=sum/k;        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        ps[i][i]=1./(s1+1.);
  }        /* Computing other pijs */
 /*********** Tricode ****************************/        for(j=1; j<i; j++)
 void tricode(int *Tvar, int **nbcode, int imx)          ps[i][j]= exp(ps[i][j])*ps[i][i];
 {        for(j=i+1; j<=nlstate+ndeath; j++)
   int Ndum[20],ij=1, k, j, i;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   int cptcode=0;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   cptcoveff=0;      } /* end i */
        
   for (k=0; k<19; k++) Ndum[k]=0;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   for (k=1; k<=7; k++) ncodemax[k]=0;        for(jj=1; jj<= nlstate+ndeath; jj++){
           ps[ii][jj]=0;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          ps[ii][ii]=1;
     for (i=1; i<=imx; i++) {        }
       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;      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
     }      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
       /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
     for (i=0; i<=cptcode; i++) {      /*   } */
       if(Ndum[i]!=0) ncodemax[j]++;      /*   printf("\n "); */
     }      /* } */
     ij=1;      /* printf("\n ");printf("%lf ",cov[2]);*/
       /*
         for(i=1; i<= npar; i++) printf("%f ",x[i]);
     for (i=1; i<=ncodemax[j]; i++) {        goto end;*/
       for (k=0; k<=19; k++) {      return ps;
         if (Ndum[k] != 0) {  }
           nbcode[Tvar[j]][ij]=k;  
           ij++;  /**************** Product of 2 matrices ******************/
         }  
         if (ij > ncodemax[j]) break;  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
       }    {
     }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   }         b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
  for (k=0; k<19; k++) Ndum[k]=0;       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
  for (i=1; i<=ncovmodel-2; i++) {    int i, j, k;
       ij=Tvar[i];    for(i=nrl; i<= nrh; i++)
       Ndum[ij]++;      for(k=ncolol; k<=ncoloh; k++){
     }        out[i][k]=0.;
         for(j=ncl; j<=nch; j++)
  ij=1;          out[i][k] +=in[i][j]*b[j][k];
  for (i=1; i<=10; i++) {      }
    if((Ndum[i]!=0) && (i<=ncov)){    return out;
      Tvaraff[ij]=i;  }
      ij++;  
    }  
  }  /************* Higher Matrix Product ***************/
    
     cptcoveff=ij-1;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 }  {
     /* Computes the transition matrix starting at age 'age' over 
 /*********** Health Expectancies ****************/       'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)       nhstepm*hstepm matrices. 
 {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   /* Health expectancies */       (typically every 2 years instead of every month which is too big 
   int i, j, nhstepm, hstepm, h;       for the memory).
   double age, agelim,hf;       Model is determined by parameters x and covariates have to be 
   double ***p3mat;       included manually here. 
    
   fprintf(ficreseij,"# Health expectancies\n");       */
   fprintf(ficreseij,"# Age");  
   for(i=1; i<=nlstate;i++)    int i, j, d, h, k;
     for(j=1; j<=nlstate;j++)    double **out, cov[NCOVMAX+1];
       fprintf(ficreseij," %1d-%1d",i,j);    double **newm;
   fprintf(ficreseij,"\n");  
     /* Hstepm could be zero and should return the unit matrix */
   hstepm=1*YEARM; /*  Every j years of age (in month) */    for (i=1;i<=nlstate+ndeath;i++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
   agelim=AGESUP;        po[i][j][0]=(i==j ? 1.0 : 0.0);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      }
     /* nhstepm age range expressed in number of stepm */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    for(h=1; h <=nhstepm; h++){
     /* Typically if 20 years = 20*12/6=40 stepm */      for(d=1; d <=hstepm; d++){
     if (stepm >= YEARM) hstepm=1;        newm=savm;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */        /* Covariates have to be included here again */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        cov[1]=1.;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        for (k=1; k<=cptcovn;k++) 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            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];
     for(i=1; i<=nlstate;i++)        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
       for(j=1; j<=nlstate;j++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){  
           eij[i][j][(int)age] +=p3mat[i][j][h];  
         }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
            /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     hf=1;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     if (stepm >= YEARM) hf=stepm/YEARM;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     fprintf(ficreseij,"%.0f",age );        savm=oldm;
     for(i=1; i<=nlstate;i++)        oldm=newm;
       for(j=1; j<=nlstate;j++){      }
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);      for(i=1; i<=nlstate+ndeath; i++)
       }        for(j=1;j<=nlstate+ndeath;j++) {
     fprintf(ficreseij,"\n");          po[i][j][h]=newm[i][j];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   }        }
 }      /*printf("h=%d ",h);*/
     } /* end h */
 /************ Variance ******************/  /*     printf("\n H=%d \n",h); */
 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)    return po;
 {  }
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;  /*************** log-likelihood *************/
   double **dnewm,**doldm;  double func( double *x)
   int i, j, nhstepm, hstepm, h;  {
   int k, cptcode;    int i, ii, j, k, mi, d, kk;
   double *xp;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **gp, **gm;    double **out;
   double ***gradg, ***trgradg;    double sw; /* Sum of weights */
   double ***p3mat;    double lli; /* Individual log likelihood */
   double age,agelim;    int s1, s2;
   int theta;    double bbh, survp;
     long ipmx;
    fprintf(ficresvij,"# Covariances of life expectancies\n");    /*extern weight */
   fprintf(ficresvij,"# Age");    /* We are differentiating ll according to initial status */
   for(i=1; i<=nlstate;i++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for(j=1; j<=nlstate;j++)    /*for(i=1;i<imx;i++) 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      printf(" %d\n",s[4][i]);
   fprintf(ficresvij,"\n");    */
     cov[1]=1.;
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   doldm=matrix(1,nlstate,1,nlstate);  
      if(mle==1){
   hstepm=1*YEARM; /* Every year of age */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        /* Computes the values of the ncovmodel covariates of the model
   agelim = AGESUP;           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */           to be observed in j being in i according to the model.
     if (stepm >= YEARM) hstepm=1;         */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          cov[2+k]=covar[Tvar[k]][i];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        }
     gp=matrix(0,nhstepm,1,nlstate);        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
     gm=matrix(0,nhstepm,1,nlstate);           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
            has been calculated etc */
     for(theta=1; theta <=npar; theta++){        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++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                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++){
       if (popbased==1) {            newm=savm;
         for(i=1; i<=nlstate;i++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           prlim[i][i]=probs[(int)age][i][ij];            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++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(h=0; h<=nhstepm; h++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            savm=oldm;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            oldm=newm;
         }          } /* end mult */
       }        
              /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       for(i=1; i<=npar; i++) /* Computes gradient */          /* But now since version 0.9 we anticipate for bias at large stepm.
         xp[i] = x[i] - (i==theta ?delti[theta]:0);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);             * (in months) between two waves is not a multiple of stepm, we rounded to 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);           * 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
       if (popbased==1) {           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         for(i=1; i<=nlstate;i++)           * probability in order to take into account the bias as a fraction of the way
           prlim[i][i]=probs[(int)age][i][ij];           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       }           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
       for(j=1; j<= nlstate; j++){           * For stepm > 1 the results are less biased than in previous versions. 
         for(h=0; h<=nhstepm; h++){           */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          s1=s[mw[mi][i]][i];
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          s2=s[mw[mi+1][i]][i];
         }          bbh=(double)bh[mi][i]/(double)stepm; 
       }          /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
       for(j=1; j<= nlstate; j++)           */
         for(h=0; h<=nhstepm; h++){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          if( s2 > nlstate){ 
         }            /* i.e. if s2 is a death state and if the date of death is known 
     } /* End theta */               then the contribution to the likelihood is the probability to 
                die between last step unit time and current  step unit time, 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);               which is also equal to probability to die before dh 
                minus probability to die before dh-stepm . 
     for(h=0; h<=nhstepm; h++)               In version up to 0.92 likelihood was computed
       for(j=1; j<=nlstate;j++)          as if date of death was unknown. Death was treated as any other
         for(theta=1; theta <=npar; theta++)          health state: the date of the interview describes the actual state
           trgradg[h][j][theta]=gradg[h][theta][j];          and not the date of a change in health state. The former idea was
           to consider that at each interview the state was recorded
     for(i=1;i<=nlstate;i++)          (healthy, disable or death) and IMaCh was corrected; but when we
       for(j=1;j<=nlstate;j++)          introduced the exact date of death then we should have modified
         vareij[i][j][(int)age] =0.;          the contribution of an exact death to the likelihood. This new
     for(h=0;h<=nhstepm;h++){          contribution is smaller and very dependent of the step unit
       for(k=0;k<=nhstepm;k++){          stepm. It is no more the probability to die between last interview
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          and month of death but the probability to survive from last
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          interview up to one month before death multiplied by the
         for(i=1;i<=nlstate;i++)          probability to die within a month. Thanks to Chris
           for(j=1;j<=nlstate;j++)          Jackson for correcting this bug.  Former versions increased
             vareij[i][j][(int)age] += doldm[i][j];          mortality artificially. The bad side is that we add another loop
       }          which slows down the processing. The difference can be up to 10%
     }          lower mortality.
     h=1;            */
     if (stepm >= YEARM) h=stepm/YEARM;            lli=log(out[s1][s2] - savm[s1][s2]);
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){          } else if  (s2==-2) {
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            for (j=1,survp=0. ; j<=nlstate; j++) 
       }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     fprintf(ficresvij,"\n");            /*survp += out[s1][j]; */
     free_matrix(gp,0,nhstepm,1,nlstate);            lli= log(survp);
     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);          else if  (s2==-4) { 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (j=3,survp=0. ; j<=nlstate; j++)  
   } /* End age */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
              lli= log(survp); 
   free_vector(xp,1,npar);          } 
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);          else if  (s2==-5) { 
             for (j=1,survp=0. ; j<=2; j++)  
 }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             lli= log(survp); 
 /************ 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)          
 {          else{
   /* Variance of prevalence limit */            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            /*  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 */
   double **newm;          } 
   double **dnewm,**doldm;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   int i, j, nhstepm, hstepm;          /*if(lli ==000.0)*/
   int k, cptcode;          /*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); */
   double *xp;          ipmx +=1;
   double *gp, *gm;          sw += weight[i];
   double **gradg, **trgradg;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double age,agelim;        } /* end of wave */
   int theta;      } /* end of individual */
        }  else if(mle==2){
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fprintf(ficresvpl,"# Age");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for(i=1; i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
       fprintf(ficresvpl," %1d-%1d",i,i);          for (ii=1;ii<=nlstate+ndeath;ii++)
   fprintf(ficresvpl,"\n");            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   xp=vector(1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   dnewm=matrix(1,nlstate,1,npar);            }
   doldm=matrix(1,nlstate,1,nlstate);          for(d=0; d<=dh[mi][i]; d++){
              newm=savm;
   hstepm=1*YEARM; /* Every year of age */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            for (kk=1; kk<=cptcovage;kk++) {
   agelim = AGESUP;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     if (stepm >= YEARM) hstepm=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            savm=oldm;
     gradg=matrix(1,npar,1,nlstate);            oldm=newm;
     gp=vector(1,nlstate);          } /* end mult */
     gm=vector(1,nlstate);        
           s1=s[mw[mi][i]][i];
     for(theta=1; theta <=npar; theta++){          s2=s[mw[mi+1][i]][i];
       for(i=1; i<=npar; i++){ /* Computes gradient */          bbh=(double)bh[mi][i]/(double)stepm; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          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 */
       }          ipmx +=1;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          sw += weight[i];
       for(i=1;i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         gp[i] = prlim[i][i];        } /* end of wave */
          } /* end of individual */
       for(i=1; i<=npar; i++) /* Computes gradient */    }  else if(mle==3){  /* exponential inter-extrapolation */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        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++){
         gm[i] = prlim[i][i];          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
       for(i=1;i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     } /* End theta */            }
           for(d=0; d<dh[mi][i]; d++){
     trgradg =matrix(1,nlstate,1,npar);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(j=1; j<=nlstate;j++)            for (kk=1; kk<=cptcovage;kk++) {
       for(theta=1; theta <=npar; theta++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         trgradg[j][theta]=gradg[theta][j];            }
             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));
       varpl[i][(int)age] =0.;            savm=oldm;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            oldm=newm;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          } /* end mult */
     for(i=1;i<=nlstate;i++)        
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     fprintf(ficresvpl,"%.0f ",age );          bbh=(double)bh[mi][i]/(double)stepm; 
     for(i=1; i<=nlstate;i++)          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 */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          ipmx +=1;
     fprintf(ficresvpl,"\n");          sw += weight[i];
     free_vector(gp,1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     free_vector(gm,1,nlstate);        } /* end of wave */
     free_matrix(gradg,1,npar,1,nlstate);      } /* end of individual */
     free_matrix(trgradg,1,nlstate,1,npar);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   } /* End age */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_vector(xp,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
   free_matrix(doldm,1,nlstate,1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   free_matrix(dnewm,1,nlstate,1,nlstate);            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);
             }
 /************ Variance of one-step probabilities  ******************/          for(d=0; d<dh[mi][i]; d++){
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)            newm=savm;
 {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i, j;            for (kk=1; kk<=cptcovage;kk++) {
   int k=0, cptcode;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double **dnewm,**doldm;            }
   double *xp;          
   double *gp, *gm;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double **gradg, **trgradg;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double age,agelim, cov[NCOVMAX];            savm=oldm;
   int theta;            oldm=newm;
   char fileresprob[FILENAMELENGTH];          } /* end mult */
         
   strcpy(fileresprob,"prob");          s1=s[mw[mi][i]][i];
   strcat(fileresprob,fileres);          s2=s[mw[mi+1][i]][i];
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          if( s2 > nlstate){ 
     printf("Problem with resultfile: %s\n", fileresprob);            lli=log(out[s1][s2] - savm[s1][s2]);
   }          }else{
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            }
           ipmx +=1;
   xp=vector(1,npar);          sw += weight[i];
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));  /*      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 */
   cov[1]=1;      } /* end of individual */
   for (age=bage; age<=fage; age ++){    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     cov[2]=age;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     gradg=matrix(1,npar,1,9);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     trgradg=matrix(1,9,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          for (ii=1;ii<=nlstate+ndeath;ii++)
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            for (j=1;j<=nlstate+ndeath;j++){
                  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(theta=1; theta <=npar; theta++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1; i<=npar; i++)            }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for(d=0; d<dh[mi][i]; d++){
                  newm=savm;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                for (kk=1; kk<=cptcovage;kk++) {
       k=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(i=1; i<= (nlstate+ndeath); i++){            }
         for(j=1; j<=(nlstate+ndeath);j++){          
            k=k+1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           gp[k]=pmmij[i][j];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
       }            oldm=newm;
           } /* 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];
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          ipmx +=1;
       k=0;          sw += weight[i];
       for(i=1; i<=(nlstate+ndeath); i++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(j=1; j<=(nlstate+ndeath);j++){          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
           k=k+1;        } /* end of wave */
           gm[k]=pmmij[i][j];      } /* end of individual */
         }    } /* End of if */
       }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
          /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      return -l;
     }  }
   
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  /*************** log-likelihood *************/
       for(theta=1; theta <=npar; theta++)  double funcone( double *x)
       trgradg[j][theta]=gradg[theta][j];  {
      /* Same as likeli but slower because of a lot of printf and if */
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    int i, ii, j, k, mi, d, kk;
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     double **out;
      pmij(pmmij,cov,ncovmodel,x,nlstate);    double lli; /* Individual log likelihood */
     double llt;
      k=0;    int s1, s2;
      for(i=1; i<=(nlstate+ndeath); i++){    double bbh, survp;
        for(j=1; j<=(nlstate+ndeath);j++){    /*extern weight */
          k=k+1;    /* We are differentiating ll according to initial status */
          gm[k]=pmmij[i][j];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         }    /*for(i=1;i<imx;i++) 
      }      printf(" %d\n",s[4][i]);
          */
      /*printf("\n%d ",(int)age);    cov[1]=1.;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  
            for(k=1; k<=nlstate; k++) ll[k]=0.;
   
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      }*/      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
   fprintf(ficresprob,"\n%d ",(int)age);        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          }
   }        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          for (kk=1; kk<=cptcovage;kk++) {
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          }
 }          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
  free_vector(xp,1,npar);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 fclose(ficresprob);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
  exit(0);          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
 }          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
           savm=oldm;
 /***********************************************/          oldm=newm;
 /**************** Main Program *****************/        } /* end mult */
 /***********************************************/        
         s1=s[mw[mi][i]][i];
 int main(int argc, char *argv[])        s2=s[mw[mi+1][i]][i];
 {        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;         * is higher than the multiple of stepm and negative otherwise.
   double agedeb, agefin,hf;         */
   double agemin=1.e20, agemax=-1.e20;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
   double fret;        } else if  (s2==-2) {
   double **xi,tmp,delta;          for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double dum; /* Dummy variable */          lli= log(survp);
   double ***p3mat;        }else if (mle==1){
   int *indx;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   char line[MAXLINE], linepar[MAXLINE];        } else if(mle==2){
   char title[MAXLINE];          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 */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];        } else if(mle==3){  /* exponential inter-extrapolation */
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
          } else if (mle==4){  /* mle=4 no inter-extrapolation */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];;          lli=log(out[s1][s2]); /* Original formula */
         } else{  /* mle=0 back to 1 */
   char filerest[FILENAMELENGTH];          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   char fileregp[FILENAMELENGTH];          /*lli=log(out[s1][s2]); */ /* Original formula */
   char popfile[FILENAMELENGTH];        } /* End of if */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        ipmx +=1;
   int firstobs=1, lastobs=10;        sw += weight[i];
   int sdeb, sfin; /* Status at beginning and end */        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int c,  h , cpt,l;        /*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]); */
   int ju,jl, mi;        if(globpr){
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;   %11.6f %11.6f %11.6f ", \
   int mobilav=0,popforecast=0;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   int hstepm, nhstepm;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   int *popage;/*boolprev=0 if date and zero if wave*/          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;            llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   double bage, fage, age, agelim, agebase;          }
   double ftolpl=FTOL;          fprintf(ficresilk," %10.6f\n", -llt);
   double **prlim;        }
   double *severity;      } /* end of wave */
   double ***param; /* Matrix of parameters */    } /* end of individual */
   double  *p;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   double **matcov; /* Matrix of covariance */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   double ***delti3; /* Scale */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   double *delti; /* Scale */    if(globpr==0){ /* First time we count the contributions and weights */
   double ***eij, ***vareij;      gipmx=ipmx;
   double **varpl; /* Variances of prevalence limits by age */      gsw=sw;
   double *epj, vepp;    }
   double kk1, kk2;    return -l;
   double *popeffectif,*popcount;  }
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;  
   double yp,yp1,yp2;  
   /*************** function likelione ***********/
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   char *alph[]={"a","a","b","c","d","e"}, str[4];  {
     /* This routine should help understanding what is done with 
        the selection of individuals/waves and
   char z[1]="c", occ;       to check the exact contribution to the likelihood.
 #include <sys/time.h>       Plotting could be done.
 #include <time.h>     */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    int k;
    
   /* long total_usecs;    if(*globpri !=0){ /* Just counts and sums, no printings */
   struct timeval start_time, end_time;      strcpy(fileresilk,"ilk"); 
        strcat(fileresilk,fileres);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   printf("\n%s",version);      }
   if(argc <=1){      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");
     printf("\nEnter the parameter file name: ");      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     scanf("%s",pathtot);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   }      for(k=1; k<=nlstate; k++) 
   else{        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     strcpy(pathtot,argv[1]);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   }    }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  
   /*cygwin_split_path(pathtot,path,optionfile);    *fretone=(*funcone)(p);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    if(*globpri !=0){
   /* cutv(path,optionfile,pathtot,'\\');*/      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      fflush(fichtm); 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    } 
   chdir(path);    return;
   replace(pathc,path);  }
   
 /*-------- arguments in the command line --------*/  
   /*********** Maximum Likelihood Estimation ***************/
   strcpy(fileres,"r");  
   strcat(fileres, optionfilefiname);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   strcat(fileres,".txt");    /* Other files have txt extension */  {
     int i,j, iter;
   /*---------arguments file --------*/    double **xi;
     double fret;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    double fretone; /* Only one call to likelihood */
     printf("Problem with optionfile %s\n",optionfile);    /*  char filerespow[FILENAMELENGTH];*/
     goto end;    xi=matrix(1,npar,1,npar);
   }    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
   strcpy(filereso,"o");        xi[i][j]=(i==j ? 1.0 : 0.0);
   strcat(filereso,fileres);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   if((ficparo=fopen(filereso,"w"))==NULL) {    strcpy(filerespow,"pow"); 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    strcat(filerespow,fileres);
   }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
   /* Reads comments: lines beginning with '#' */      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     fgets(line, MAXLINE, ficpar);    for (i=1;i<=nlstate;i++)
     puts(line);      for(j=1;j<=nlstate+ndeath;j++)
     fputs(line,ficparo);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   }    fprintf(ficrespow,"\n");
   ungetc(c,ficpar);  
     powell(p,xi,npar,ftol,&iter,&fret,func);
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);  
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    free_matrix(xi,1,npar,1,npar);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    fclose(ficrespow);
 while((c=getc(ficpar))=='#' && c!= EOF){    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     ungetc(c,ficpar);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fgets(line, MAXLINE, ficpar);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     puts(line);  
     fputs(line,ficparo);  }
   }  
   ungetc(c,ficpar);  /**** Computes Hessian and covariance matrix ***/
    void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
      {
   covar=matrix(0,NCOVMAX,1,n);    double  **a,**y,*x,pd;
   cptcovn=0;    double **hess;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    int i, j,jk;
     int *indx;
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
      double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   /* Read guess parameters */    void lubksb(double **a, int npar, int *indx, double b[]) ;
   /* Reads comments: lines beginning with '#' */    void ludcmp(double **a, int npar, int *indx, double *d) ;
   while((c=getc(ficpar))=='#' && c!= EOF){    double gompertz(double p[]);
     ungetc(c,ficpar);    hess=matrix(1,npar,1,npar);
     fgets(line, MAXLINE, ficpar);  
     puts(line);    printf("\nCalculation of the hessian matrix. Wait...\n");
     fputs(line,ficparo);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   }    for (i=1;i<=npar;i++){
   ungetc(c,ficpar);      printf("%d",i);fflush(stdout);
        fprintf(ficlog,"%d",i);fflush(ficlog);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);     
     for(i=1; i <=nlstate; i++)       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     for(j=1; j <=nlstate+ndeath-1; j++){      
       fscanf(ficpar,"%1d%1d",&i1,&j1);      /*  printf(" %f ",p[i]);
       fprintf(ficparo,"%1d%1d",i1,j1);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       printf("%1d%1d",i,j);    }
       for(k=1; k<=ncovmodel;k++){    
         fscanf(ficpar," %lf",&param[i][j][k]);    for (i=1;i<=npar;i++) {
         printf(" %lf",param[i][j][k]);      for (j=1;j<=npar;j++)  {
         fprintf(ficparo," %lf",param[i][j][k]);        if (j>i) { 
       }          printf(".%d%d",i,j);fflush(stdout);
       fscanf(ficpar,"\n");          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       printf("\n");          hess[i][j]=hessij(p,delti,i,j,func,npar);
       fprintf(ficparo,"\n");          
     }          hess[j][i]=hess[i][j];    
            /*printf(" %lf ",hess[i][j]);*/
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        }
       }
   p=param[1][1];    }
      printf("\n");
   /* Reads comments: lines beginning with '#' */    fprintf(ficlog,"\n");
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fgets(line, MAXLINE, ficpar);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     puts(line);    
     fputs(line,ficparo);    a=matrix(1,npar,1,npar);
   }    y=matrix(1,npar,1,npar);
   ungetc(c,ficpar);    x=vector(1,npar);
     indx=ivector(1,npar);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    for (i=1;i<=npar;i++)
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   for(i=1; i <=nlstate; i++){    ludcmp(a,npar,indx,&pd);
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);    for (j=1;j<=npar;j++) {
       printf("%1d%1d",i,j);      for (i=1;i<=npar;i++) x[i]=0;
       fprintf(ficparo,"%1d%1d",i1,j1);      x[j]=1;
       for(k=1; k<=ncovmodel;k++){      lubksb(a,npar,indx,x);
         fscanf(ficpar,"%le",&delti3[i][j][k]);      for (i=1;i<=npar;i++){ 
         printf(" %le",delti3[i][j][k]);        matcov[i][j]=x[i];
         fprintf(ficparo," %le",delti3[i][j][k]);      }
       }    }
       fscanf(ficpar,"\n");  
       printf("\n");    printf("\n#Hessian matrix#\n");
       fprintf(ficparo,"\n");    fprintf(ficlog,"\n#Hessian matrix#\n");
     }    for (i=1;i<=npar;i++) { 
   }      for (j=1;j<=npar;j++) { 
   delti=delti3[1][1];        printf("%.3e ",hess[i][j]);
          fprintf(ficlog,"%.3e ",hess[i][j]);
   /* Reads comments: lines beginning with '#' */      }
   while((c=getc(ficpar))=='#' && c!= EOF){      printf("\n");
     ungetc(c,ficpar);      fprintf(ficlog,"\n");
     fgets(line, MAXLINE, ficpar);    }
     puts(line);  
     fputs(line,ficparo);    /* Recompute Inverse */
   }    for (i=1;i<=npar;i++)
   ungetc(c,ficpar);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
      ludcmp(a,npar,indx,&pd);
   matcov=matrix(1,npar,1,npar);  
   for(i=1; i <=npar; i++){    /*  printf("\n#Hessian matrix recomputed#\n");
     fscanf(ficpar,"%s",&str);  
     printf("%s",str);    for (j=1;j<=npar;j++) {
     fprintf(ficparo,"%s",str);      for (i=1;i<=npar;i++) x[i]=0;
     for(j=1; j <=i; j++){      x[j]=1;
       fscanf(ficpar," %le",&matcov[i][j]);      lubksb(a,npar,indx,x);
       printf(" %.5le",matcov[i][j]);      for (i=1;i<=npar;i++){ 
       fprintf(ficparo," %.5le",matcov[i][j]);        y[i][j]=x[i];
     }        printf("%.3e ",y[i][j]);
     fscanf(ficpar,"\n");        fprintf(ficlog,"%.3e ",y[i][j]);
     printf("\n");      }
     fprintf(ficparo,"\n");      printf("\n");
   }      fprintf(ficlog,"\n");
   for(i=1; i <=npar; i++)    }
     for(j=i+1;j<=npar;j++)    */
       matcov[i][j]=matcov[j][i];  
        free_matrix(a,1,npar,1,npar);
   printf("\n");    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
     free_ivector(indx,1,npar);
     /*-------- data file ----------*/    free_matrix(hess,1,npar,1,npar);
     if((ficres =fopen(fileres,"w"))==NULL) {  
       printf("Problem with resultfile: %s\n", fileres);goto end;  
     }  }
     fprintf(ficres,"#%s\n",version);  
      /*************** hessian matrix ****************/
     if((fic=fopen(datafile,"r"))==NULL)    {  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       printf("Problem with datafile: %s\n", datafile);goto end;  {
     }    int i;
     int l=1, lmax=20;
     n= lastobs;    double k1,k2;
     severity = vector(1,maxwav);    double p2[MAXPARM+1]; /* identical to x */
     outcome=imatrix(1,maxwav+1,1,n);    double res;
     num=ivector(1,n);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     moisnais=vector(1,n);    double fx;
     annais=vector(1,n);    int k=0,kmax=10;
     moisdc=vector(1,n);    double l1;
     andc=vector(1,n);  
     agedc=vector(1,n);    fx=func(x);
     cod=ivector(1,n);    for (i=1;i<=npar;i++) p2[i]=x[i];
     weight=vector(1,n);    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      l1=pow(10,l);
     mint=matrix(1,maxwav,1,n);      delts=delt;
     anint=matrix(1,maxwav,1,n);      for(k=1 ; k <kmax; k=k+1){
     s=imatrix(1,maxwav+1,1,n);        delt = delta*(l1*k);
     adl=imatrix(1,maxwav+1,1,n);            p2[theta]=x[theta] +delt;
     tab=ivector(1,NCOVMAX);        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
     ncodemax=ivector(1,8);        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
     i=1;        /*res= (k1-2.0*fx+k2)/delt/delt; */
     while (fgets(line, MAXLINE, fic) != NULL)    {        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       if ((i >= firstobs) && (i <=lastobs)) {        
          #ifdef DEBUGHESS
         for (j=maxwav;j>=1;j--){        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);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        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);
           strcpy(line,stra);  #endif
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         }          k=kmax;
                }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          k=kmax; l=lmax*10.;
         }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          delts=delt;
         }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      }
         for (j=ncov;j>=1;j--){    }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    delti[theta]=delts;
         }    return res; 
         num[i]=atol(stra);    
          }
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   {
         i=i+1;    int i;
       }    int l=1, l1, lmax=20;
     }    double k1,k2,k3,k4,res,fx;
     /* printf("ii=%d", ij);    double p2[MAXPARM+1];
        scanf("%d",i);*/    int k;
   imx=i-1; /* Number of individuals */  
     fx=func(x);
   /* for (i=1; i<=imx; i++){    for (k=1; k<=2; k++) {
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      for (i=1;i<=npar;i++) p2[i]=x[i];
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      p2[thetai]=x[thetai]+delti[thetai]/k;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     }      k1=func(p2)-fx;
     
     for (i=1; i<=imx; i++)      p2[thetai]=x[thetai]+delti[thetai]/k;
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
   /* Calculation of the number of parameter from char model*/    
   Tvar=ivector(1,15);      p2[thetai]=x[thetai]-delti[thetai]/k;
   Tprod=ivector(1,15);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   Tvaraff=ivector(1,15);      k3=func(p2)-fx;
   Tvard=imatrix(1,15,1,2);    
   Tage=ivector(1,15);            p2[thetai]=x[thetai]-delti[thetai]/k;
          p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   if (strlen(model) >1){      k4=func(p2)-fx;
     j=0, j1=0, k1=1, k2=1;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     j=nbocc(model,'+');  #ifdef DEBUG
     j1=nbocc(model,'*');      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);
     cptcovn=j+1;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     cptcovprod=j1;  #endif
        }
        return res;
     strcpy(modelsav,model);  }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  
       printf("Error. Non available option model=%s ",model);  /************** Inverse of matrix **************/
       goto end;  void ludcmp(double **a, int n, int *indx, double *d) 
     }  { 
        int i,imax,j,k; 
     for(i=(j+1); i>=1;i--){    double big,dum,sum,temp; 
       cutv(stra,strb,modelsav,'+');    double *vv; 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);   
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    vv=vector(1,n); 
       /*scanf("%d",i);*/    *d=1.0; 
       if (strchr(strb,'*')) {    for (i=1;i<=n;i++) { 
         cutv(strd,strc,strb,'*');      big=0.0; 
         if (strcmp(strc,"age")==0) {      for (j=1;j<=n;j++) 
           cptcovprod--;        if ((temp=fabs(a[i][j])) > big) big=temp; 
           cutv(strb,stre,strd,'V');      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           Tvar[i]=atoi(stre);      vv[i]=1.0/big; 
           cptcovage++;    } 
             Tage[cptcovage]=i;    for (j=1;j<=n;j++) { 
             /*printf("stre=%s ", stre);*/      for (i=1;i<j;i++) { 
         }        sum=a[i][j]; 
         else if (strcmp(strd,"age")==0) {        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           cptcovprod--;        a[i][j]=sum; 
           cutv(strb,stre,strc,'V');      } 
           Tvar[i]=atoi(stre);      big=0.0; 
           cptcovage++;      for (i=j;i<=n;i++) { 
           Tage[cptcovage]=i;        sum=a[i][j]; 
         }        for (k=1;k<j;k++) 
         else {          sum -= a[i][k]*a[k][j]; 
           cutv(strb,stre,strc,'V');        a[i][j]=sum; 
           Tvar[i]=ncov+k1;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           cutv(strb,strc,strd,'V');          big=dum; 
           Tprod[k1]=i;          imax=i; 
           Tvard[k1][1]=atoi(strc);        } 
           Tvard[k1][2]=atoi(stre);      } 
           Tvar[cptcovn+k2]=Tvard[k1][1];      if (j != imax) { 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        for (k=1;k<=n;k++) { 
           for (k=1; k<=lastobs;k++)          dum=a[imax][k]; 
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          a[imax][k]=a[j][k]; 
           k1++;          a[j][k]=dum; 
           k2=k2+2;        } 
         }        *d = -(*d); 
       }        vv[imax]=vv[j]; 
       else {      } 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      indx[j]=imax; 
        /*  scanf("%d",i);*/      if (a[j][j] == 0.0) a[j][j]=TINY; 
       cutv(strd,strc,strb,'V');      if (j != n) { 
       Tvar[i]=atoi(strc);        dum=1.0/(a[j][j]); 
       }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       strcpy(modelsav,stra);        } 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    } 
         scanf("%d",i);*/    free_vector(vv,1,n);  /* Doesn't work */
     }  ;
 }  } 
    
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  void lubksb(double **a, int n, int *indx, double b[]) 
   printf("cptcovprod=%d ", cptcovprod);  { 
   scanf("%d ",i);*/    int i,ii=0,ip,j; 
     fclose(fic);    double sum; 
    
     /*  if(mle==1){*/    for (i=1;i<=n;i++) { 
     if (weightopt != 1) { /* Maximisation without weights*/      ip=indx[i]; 
       for(i=1;i<=n;i++) weight[i]=1.0;      sum=b[ip]; 
     }      b[ip]=b[i]; 
     /*-calculation of age at interview from date of interview and age at death -*/      if (ii) 
     agev=matrix(1,maxwav,1,imx);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
    for (i=1; i<=imx; i++)      b[i]=sum; 
      for(m=2; (m<= maxwav); m++)    } 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    for (i=n;i>=1;i--) { 
          anint[m][i]=9999;      sum=b[i]; 
          s[m][i]=-1;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
        }      b[i]=sum/a[i][i]; 
        } 
     for (i=1; i<=imx; i++)  {  } 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){  void pstamp(FILE *fichier)
         if(s[m][i] >0){  {
           if (s[m][i] == nlstate+1) {    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
             if(agedc[i]>0)  }
               if(moisdc[i]!=99 && andc[i]!=9999)  
               agev[m][i]=agedc[i];  /************ Frequencies ********************/
             else {  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[])
               if (andc[i]!=9999){  {  /* Some frequencies */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    
               agev[m][i]=-1;    int i, m, jk, k1,i1, j1, bool, z1,j;
               }    int first;
             }    double ***freq; /* Frequencies */
           }    double *pp, **prop;
           else if(s[m][i] !=9){ /* Should no more exist */    double pos,posprop, k2, dateintsum=0,k2cpt=0;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    char fileresp[FILENAMELENGTH];
             if(mint[m][i]==99 || anint[m][i]==9999)    
               agev[m][i]=1;    pp=vector(1,nlstate);
             else if(agev[m][i] <agemin){    prop=matrix(1,nlstate,iagemin,iagemax+3);
               agemin=agev[m][i];    strcpy(fileresp,"p");
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    strcat(fileresp,fileres);
             }    if((ficresp=fopen(fileresp,"w"))==NULL) {
             else if(agev[m][i] >agemax){      printf("Problem with prevalence resultfile: %s\n", fileresp);
               agemax=agev[m][i];      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      exit(0);
             }    }
             /*agev[m][i]=anint[m][i]-annais[i];*/    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
             /*   agev[m][i] = age[i]+2*m;*/    j1=0;
           }    
           else { /* =9 */    j=cptcoveff;
             agev[m][i]=1;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
             s[m][i]=-1;  
           }    first=1;
         }  
         else /*= 0 Unknown */    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
           agev[m][i]=1;    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
       }    /*    j1++;
      */
     }    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
     for (i=1; i<=imx; i++)  {        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       for(m=1; (m<= maxwav); m++){          scanf("%d", i);*/
         if (s[m][i] > (nlstate+ndeath)) {        for (i=-5; i<=nlstate+ndeath; i++)  
           printf("Error: Wrong value in nlstate or ndeath\n");            for (jk=-5; jk<=nlstate+ndeath; jk++)  
           goto end;            for(m=iagemin; m <= iagemax+3; m++)
         }              freq[i][jk][m]=0;
       }        
     }        for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            prop[i][m]=0;
         
     free_vector(severity,1,maxwav);        dateintsum=0;
     free_imatrix(outcome,1,maxwav+1,1,n);        k2cpt=0;
     free_vector(moisnais,1,n);        for (i=1; i<=imx; i++) {
     free_vector(annais,1,n);          bool=1;
     /* free_matrix(mint,1,maxwav,1,n);          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
        free_matrix(anint,1,maxwav,1,n);*/            for (z1=1; z1<=cptcoveff; z1++)       
     free_vector(moisdc,1,n);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
     free_vector(andc,1,n);                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
                 bool=0;
                    /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
     wav=ivector(1,imx);                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
     dh=imatrix(1,lastpass-firstpass+1,1,imx);                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
     mw=imatrix(1,lastpass-firstpass+1,1,imx);                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
                  } 
     /* Concatenates waves */          }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);   
           if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
       Tcode=ivector(1,100);              k2=anint[m][i]+(mint[m][i]/12.);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       ncodemax[1]=1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                      if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
    codtab=imatrix(1,100,1,10);                if (m<lastpass) {
    h=0;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
    m=pow(2,cptcoveff);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                  }
    for(k=1;k<=cptcoveff; k++){                
      for(i=1; i <=(m/pow(2,k));i++){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
        for(j=1; j <= ncodemax[k]; j++){                  dateintsum=dateintsum+k2;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                  k2cpt++;
            h++;                }
            if (h>m) h=1;codtab[h][k]=j;                /*}*/
          }            }
        }          }
      }        } /* end i */
    }         
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         pstamp(ficresp);
    /*for(i=1; i <=m ;i++){        if  (cptcovn>0) {
      for(k=1; k <=cptcovn; k++){          fprintf(ficresp, "\n#********** Variable "); 
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      }          fprintf(ficresp, "**********\n#");
      printf("\n");          fprintf(ficlog, "\n#********** Variable "); 
    }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    scanf("%d",i);*/          fprintf(ficlog, "**********\n#");
            }
    /* Calculates basic frequencies. Computes observed prevalence at single age        for(i=1; i<=nlstate;i++) 
        and prints on file fileres'p'. */          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
            
            for(i=iagemin; i <= iagemax+3; i++){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          if(i==iagemax+3){
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            fprintf(ficlog,"Total");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          }else{
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            if(first==1){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              first=0;
                    printf("See log file for details...\n");
     /* For Powell, parameters are in a vector p[] starting at p[1]            }
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */            fprintf(ficlog,"Age %d", i);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          }
           for(jk=1; jk <=nlstate ; jk++){
     if(mle==1){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              pp[jk] += freq[jk][m][i]; 
     }          }
              for(jk=1; jk <=nlstate ; jk++){
     /*--------- results files --------------*/            for(m=-1, pos=0; m <=0 ; m++)
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);              pos += freq[jk][m][i];
              if(pp[jk]>=1.e-10){
               if(first==1){
    jk=1;                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
    fprintf(ficres,"# Parameters\n");              }
    printf("# Parameters\n");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
    for(i=1,jk=1; i <=nlstate; i++){            }else{
      for(k=1; k <=(nlstate+ndeath); k++){              if(first==1)
        if (k != i)                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
          {              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
            printf("%d%d ",i,k);            }
            fprintf(ficres,"%1d%1d ",i,k);          }
            for(j=1; j <=ncovmodel; j++){  
              printf("%f ",p[jk]);          for(jk=1; jk <=nlstate ; jk++){
              fprintf(ficres,"%f ",p[jk]);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
              jk++;              pp[jk] += freq[jk][m][i];
            }          }       
            printf("\n");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
            fprintf(ficres,"\n");            pos += pp[jk];
          }            posprop += prop[jk][i];
      }          }
    }          for(jk=1; jk <=nlstate ; jk++){
  if(mle==1){            if(pos>=1.e-5){
     /* Computing hessian and covariance matrix */              if(first==1)
     ftolhess=ftol; /* Usually correct */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     hesscov(matcov, p, npar, delti, ftolhess, func);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
  }            }else{
     fprintf(ficres,"# Scales\n");              if(first==1)
     printf("# Scales\n");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
      for(i=1,jk=1; i <=nlstate; i++){              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for(j=1; j <=nlstate+ndeath; j++){            }
         if (j!=i) {            if( i <= iagemax){
           fprintf(ficres,"%1d%1d",i,j);              if(pos>=1.e-5){
           printf("%1d%1d",i,j);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
           for(k=1; k<=ncovmodel;k++){                /*probs[i][jk][j1]= pp[jk]/pos;*/
             printf(" %.5e",delti[jk]);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
             fprintf(ficres," %.5e",delti[jk]);              }
             jk++;              else
           }                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
           printf("\n");            }
           fprintf(ficres,"\n");          }
         }          
       }          for(jk=-1; jk <=nlstate+ndeath; jk++)
      }            for(m=-1; m <=nlstate+ndeath; m++)
                  if(freq[jk][m][i] !=0 ) {
     k=1;              if(first==1)
     fprintf(ficres,"# Covariance\n");                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     printf("# Covariance\n");                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(i=1;i<=npar;i++){              }
       /*  if (k>nlstate) k=1;          if(i <= iagemax)
       i1=(i-1)/(ncovmodel*nlstate)+1;            fprintf(ficresp,"\n");
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          if(first==1)
       printf("%s%d%d",alph[k],i1,tab[i]);*/            printf("Others in log...\n");
       fprintf(ficres,"%3d",i);          fprintf(ficlog,"\n");
       printf("%3d",i);        }
       for(j=1; j<=i;j++){        /*}*/
         fprintf(ficres," %.5e",matcov[i][j]);    }
         printf(" %.5e",matcov[i][j]);    dateintmean=dateintsum/k2cpt; 
       }   
       fprintf(ficres,"\n");    fclose(ficresp);
       printf("\n");    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
       k++;    free_vector(pp,1,nlstate);
     }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
        /* End of Freq */
     while((c=getc(ficpar))=='#' && c!= EOF){  }
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);  /************ Prevalence ********************/
       puts(line);  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)
       fputs(line,ficparo);  {  
     }    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     ungetc(c,ficpar);       in each health status at the date of interview (if between dateprev1 and dateprev2).
         We still use firstpass and lastpass as another selection.
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    */
       
     if (fage <= 2) {    int i, m, jk, k1, i1, j1, bool, z1,j;
       bage = agemin;    double ***freq; /* Frequencies */
       fage = agemax;    double *pp, **prop;
     }    double pos,posprop; 
        double  y2; /* in fractional years */
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    int iagemin, iagemax;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    int first; /** to stop verbosity which is redirected to log file */
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  
      iagemin= (int) agemin;
     while((c=getc(ficpar))=='#' && c!= EOF){    iagemax= (int) agemax;
     ungetc(c,ficpar);    /*pp=vector(1,nlstate);*/
     fgets(line, MAXLINE, ficpar);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     puts(line);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     fputs(line,ficparo);    j1=0;
   }    
   ungetc(c,ficpar);    /*j=cptcoveff;*/
      if (cptcovn<1) {j=1;ncodemax[1]=1;}
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);    
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    first=1;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
            /*for(i1=1; i1<=ncodemax[k1];i1++){
   while((c=getc(ficpar))=='#' && c!= EOF){        j1++;*/
     ungetc(c,ficpar);        
     fgets(line, MAXLINE, ficpar);        for (i=1; i<=nlstate; i++)  
     puts(line);          for(m=iagemin; m <= iagemax+3; m++)
     fputs(line,ficparo);            prop[i][m]=0.0;
   }       
   ungetc(c,ficpar);        for (i=1; i<=imx; i++) { /* Each individual */
            bool=1;
           if  (cptcovn>0) {
    dateprev1=anprev1+mprev1/12.+jprev1/365.;            for (z1=1; z1<=cptcoveff; z1++) 
    dateprev2=anprev2+mprev2/12.+jprev2/365.;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
   fscanf(ficpar,"pop_based=%d\n",&popbased);          } 
    fprintf(ficparo,"pop_based=%d\n",popbased);            if (bool==1) { 
    fprintf(ficres,"pop_based=%d\n",popbased);              for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   while((c=getc(ficpar))=='#' && c!= EOF){              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     ungetc(c,ficpar);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fgets(line, MAXLINE, ficpar);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     puts(line);                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); 
     fputs(line,ficparo);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   }                  /*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]]);*/
   ungetc(c,ficpar);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);                  prop[s[m][i]][iagemax+3] += weight[i]; 
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);                } 
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);              }
             } /* end selection of waves */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);          }
         }
            for(i=iagemin; i <= iagemax+3; i++){  
     /*------------ gnuplot -------------*/          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     /*chdir(pathcd);*/            posprop += prop[jk][i]; 
     strcpy(optionfilegnuplot,optionfilefiname);          } 
     strcat(optionfilegnuplot,".plt");          
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          for(jk=1; jk <=nlstate ; jk++){     
       printf("Problem with file %s",optionfilegnuplot);goto end;            if( i <=  iagemax){ 
     }              if(posprop>=1.e-5){ 
 #ifdef windows                probs[i][jk][j1]= prop[jk][i]/posprop;
     fprintf(ficgp,"cd \"%s\" \n",pathc);              } else{
 #endif                if(first==1){
 m=pow(2,cptcoveff);                  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]);
  /* 1eme*/                }
   for (cpt=1; cpt<= nlstate ; cpt ++) {              }
    for (k1=1; k1<= m ; k1 ++) {            } 
           }/* end jk */ 
 #ifdef windows        }/* end 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",agemin,fage,fileres,k1-1,k1-1);      /*} *//* end i1 */
 #endif    } /* end j1 */
 #ifdef unix    
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
 #endif    /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 for (i=1; i<= nlstate ; i ++) {  }  /* End of prevalence */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  /************* Waves Concatenation ***************/
 }  
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
     for (i=1; i<= nlstate ; i ++) {  {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   else fprintf(ficgp," \%%*lf (\%%*lf)");       Death is a valid wave (if date is known).
 }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
      for (i=1; i<= nlstate ; i ++) {       and mw[mi+1][i]. dh depends on stepm.
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      int i, mi, m;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 #ifdef unix       double sum=0., jmean=0.;*/
 fprintf(ficgp,"\nset ter gif small size 400,300");    int first;
 #endif    int j, k=0,jk, ju, jl;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    double sum=0.;
    }    first=0;
   }    jmin=1e+5;
   /*2 eme*/    jmax=-1;
     jmean=0.;
   for (k1=1; k1<= m ; k1 ++) {    for(i=1; i<=imx; i++){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);      mi=0;
          m=firstpass;
     for (i=1; i<= nlstate+1 ; i ++) {      while(s[m][i] <= nlstate){
       k=2*i;        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          mw[++mi][i]=m;
       for (j=1; j<= nlstate+1 ; j ++) {        if(m >=lastpass)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          break;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        else
 }            m++;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      }/* end while */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      if (s[m][i] > nlstate){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        mi++;     /* Death is another wave */
       for (j=1; j<= nlstate+1 ; j ++) {        /* if(mi==0)  never been interviewed correctly before death */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");           /* Only death is a correct wave */
         else fprintf(ficgp," \%%*lf (\%%*lf)");        mw[mi][i]=m;
 }        }
       fprintf(ficgp,"\" t\"\" w l 0,");  
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      wav[i]=mi;
       for (j=1; j<= nlstate+1 ; j ++) {      if(mi==0){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        nbwarn++;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        if(first==0){
 }            printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          first=1;
       else fprintf(ficgp,"\" t\"\" w l 0,");        }
     }        if(first==1){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
   }        }
        } /* end mi==0 */
   /*3eme*/    } /* End individuals */
   
   for (k1=1; k1<= m ; k1 ++) {    for(i=1; i<=imx; i++){
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for(mi=1; mi<wav[i];mi++){
       k=2+nlstate*(cpt-1);        if (stepm <=0)
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);          dh[mi][i]=1;
       for (i=1; i< nlstate ; i ++) {        else{
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       }            if (agedc[i] < 2*AGESUP) {
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     }              if(j==0) j=1;  /* Survives at least one month after exam */
   }              else if(j<0){
                  nberr++;
   /* CV preval stat */                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]);
   for (k1=1; k1<= m ; k1 ++) {                j=1; /* Temporary Dangerous patch */
     for (cpt=1; cpt<nlstate ; cpt ++) {                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);
       k=3;                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       for (i=1; i< nlstate ; i ++)              }
         fprintf(ficgp,"+$%d",k+i+1);              k=k+1;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              if (j >= jmax){
                      jmax=j;
       l=3+(nlstate+ndeath)*cpt;                ijmax=i;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);              }
       for (i=1; i< nlstate ; i ++) {              if (j <= jmin){
         l=3+(nlstate+ndeath)*cpt;                jmin=j;
         fprintf(ficgp,"+$%d",l+i+1);                ijmin=i;
       }              }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                sum=sum+j;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              /*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);*/
   }              }
           }
   /* proba elementaires */          else{
    for(i=1,jk=1; i <=nlstate; i++){            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     for(k=1; k <=(nlstate+ndeath); k++){  /*        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]); */
       if (k != i) {  
         for(j=1; j <=ncovmodel; j++){            k=k+1;
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/            if (j >= jmax) {
           /*fprintf(ficgp,"%s",alph[1]);*/              jmax=j;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);              ijmax=i;
           jk++;            }
           fprintf(ficgp,"\n");            else if (j <= jmin){
         }              jmin=j;
       }              ijmin=i;
     }            }
     }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*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]);*/
   for(jk=1; jk <=m; jk++) {            if(j<0){
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);              nberr++;
    i=1;              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]);
    for(k2=1; k2<=nlstate; k2++) {              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]);
      k3=i;            }
      for(k=1; k<=(nlstate+ndeath); k++) {            sum=sum+j;
        if (k != k2){          }
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          jk= j/stepm;
 ij=1;          jl= j -jk*stepm;
         for(j=3; j <=ncovmodel; j++) {          ju= j -(jk+1)*stepm;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            if(jl==0){
             ij++;              dh[mi][i]=jk;
           }              bh[mi][i]=0;
           else            }else{ /* We want a negative bias in order to only have interpolation ie
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                    * to avoid the price of an extra matrix product in likelihood */
         }              dh[mi][i]=jk+1;
           fprintf(ficgp,")/(1");              bh[mi][i]=ju;
                    }
         for(k1=1; k1 <=nlstate; k1++){            }else{
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            if(jl <= -ju){
 ij=1;              dh[mi][i]=jk;
           for(j=3; j <=ncovmodel; j++){              bh[mi][i]=jl;       /* bias is positive if real duration
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                                   * is higher than the multiple of stepm and negative otherwise.
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                                   */
             ij++;            }
           }            else{
           else              dh[mi][i]=jk+1;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              bh[mi][i]=ju;
           }            }
           fprintf(ficgp,")");            if(dh[mi][i]==0){
         }              dh[mi][i]=1; /* At least one step */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);              bh[mi][i]=ju; /* At least one step */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");              /*  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);*/
         i=i+ncovmodel;            }
        }          } /* end if mle */
      }        }
    }      } /* end wave */
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    }
   }    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);
   fclose(ficgp);    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);
   /* end gnuplot */   }
      
 chdir(path);  /*********** Tricode ****************************/
      void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
     free_ivector(wav,1,imx);  {
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
     free_ivector(num,1,n);    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
     free_vector(agedc,1,n);     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    /* nbcode[Tvar[j]][1]= 
     fclose(ficparo);    */
     fclose(ficres);  
     /*  }*/    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
        int modmaxcovj=0; /* Modality max of covariates j */
    /*________fin mle=1_________*/    int cptcode=0; /* Modality max of covariates j */
        int modmincovj=0; /* Modality min of covariates j */
   
    
     /* No more information from the sample is required now */    cptcoveff=0; 
   /* Reads comments: lines beginning with '#' */   
   while((c=getc(ficpar))=='#' && c!= EOF){    for (k=-1; k < maxncov; k++) Ndum[k]=0;
     ungetc(c,ficpar);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
     fgets(line, MAXLINE, ficpar);  
     puts(line);    /* Loop on covariates without age and products */
     fputs(line,ficparo);    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 
   ungetc(c,ficpar);                                 modality of this covariate Vj*/ 
          ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);                                      * If product of Vn*Vm, still boolean *:
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
 /*--------- index.htm --------*/        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                         modality of the nth covariate of individual i. */
   strcpy(optionfilehtm,optionfile);        if (ij > modmaxcovj)
   strcat(optionfilehtm,".htm");          modmaxcovj=ij; 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        else if (ij < modmincovj) 
     printf("Problem with %s \n",optionfilehtm);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 );
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">          exit(1);
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>        }else
 Total number of observations=%d <br>        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
 <hr  size=\"2\" color=\"#EC5E5E\">        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 <li>Outputs files<br><br>\n        /* getting the maximum value of the modality of the covariate
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>           female is 1, then modmaxcovj=1.*/
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>      }
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>      cptcode=modmaxcovj;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>     /*for (i=0; i<=cptcode; i++) {*/
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
         }
  fprintf(fichtm," <li>Graphs</li><p>");        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
            historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
  m=cptcoveff;      } /* Ndum[-1] number of undefined modalities */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
       /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
  j1=0;      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
  for(k1=1; k1<=m;k1++){      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
    for(i1=1; i1<=ncodemax[k1];i1++){         modmincovj=3; modmaxcovj = 7;
        j1++;         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
        if (cptcovn > 0) {         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         variables V1_1 and V1_2.
          for (cpt=1; cpt<=cptcoveff;cpt++)         nbcode[Tvar[j]][ij]=k;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);         nbcode[Tvar[j]][1]=0;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         nbcode[Tvar[j]][2]=1;
        }         nbcode[Tvar[j]][3]=2;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          ij=1; /* ij is similar to i but can jumps over null modalities */
        for(cpt=1; cpt<nlstate;cpt++){      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          /*recode from 0 */
        }          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
     for(cpt=1; cpt<=nlstate;cpt++) {            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident                                       k is a modality. If we have model=V1+V1*sex 
 interval) in state (%d): v%s%d%d.gif <br>                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);              ij++;
      }          }
      for(cpt=1; cpt<=nlstate;cpt++) {          if (ij > ncodemax[j]) break; 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        }  /* end of loop on */
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      } /* 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*/  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    
 health expectancies in states (1) and (2): e%s%d.gif<br>   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    
 fprintf(fichtm,"\n</body>");    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
    }     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
  }     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
 fclose(fichtm);     Ndum[ij]++; 
    } 
   /*--------------- Prevalence limit --------------*/  
     ij=1;
   strcpy(filerespl,"pl");   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   strcat(filerespl,fileres);     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   if((ficrespl=fopen(filerespl,"w"))==NULL) {     if((Ndum[i]!=0) && (i<=ncovcol)){
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
   }       Tvaraff[ij]=i; /*For printing (unclear) */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);       ij++;
   fprintf(ficrespl,"#Prevalence limit\n");     }else
   fprintf(ficrespl,"#Age ");         Tvaraff[ij]=0;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);   }
   fprintf(ficrespl,"\n");   ij--;
     cptcoveff=ij; /*Number of total covariates*/
   prlim=matrix(1,nlstate,1,nlstate);  
   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 */  /*********** Health Expectancies ****************/
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   agebase=agemin;  
   agelim=agemax;  {
   ftolpl=1.e-10;    /* Health expectancies, no variances */
   i1=cptcoveff;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   if (cptcovn < 1){i1=1;}    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
   for(cptcov=1;cptcov<=i1;cptcov++){    double ***p3mat;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double eip;
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    pstamp(ficreseij);
         fprintf(ficrespl,"\n#******");    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
         for(j=1;j<=cptcoveff;j++)    fprintf(ficreseij,"# Age");
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for(i=1; i<=nlstate;i++){
         fprintf(ficrespl,"******\n");      for(j=1; j<=nlstate;j++){
                fprintf(ficreseij," e%1d%1d ",i,j);
         for (age=agebase; age<=agelim; age++){      }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      fprintf(ficreseij," e%1d. ",i);
           fprintf(ficrespl,"%.0f",age );    }
           for(i=1; i<=nlstate;i++)    fprintf(ficreseij,"\n");
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");    
         }    if(estepm < stepm){
       }      printf ("Problem %d lower than %d\n",estepm, stepm);
     }    }
   fclose(ficrespl);    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   /*------------- h Pij x at various ages ------------*/     * This is mainly to measure the difference between two models: for example
       * if stepm=24 months pijx are given only every 2 years and by summing them
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   if((ficrespij=fopen(filerespij,"w"))==NULL) {     * progression in between and thus overestimating or underestimating according
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;     * to the curvature of the survival function. If, for the same date, we 
   }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   printf("Computing pij: result on file '%s' \n", filerespij);     * to compare the new estimate of Life expectancy with the same linear 
       * hypothesis. A more precise result, taking into account a more precise
   stepsize=(int) (stepm+YEARM-1)/YEARM;     * curvature will be obtained if estepm is as small as stepm. */
   /*if (stepm<=24) stepsize=2;*/  
     /* For example we decided to compute the life expectancy with the smallest unit */
   agelim=AGESUP;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   hstepm=stepsize*YEARM; /* Every year of age */       nhstepm is the number of hstepm from age to agelim 
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */       nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
   k=0;       and note for a fixed period like estepm months */
   for(cptcov=1;cptcov<=i1;cptcov++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       survival function given by stepm (the optimization length). Unfortunately it
       k=k+1;       means that if the survival funtion is printed only each two years of age and if
         fprintf(ficrespij,"\n#****** ");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         for(j=1;j<=cptcoveff;j++)       results. So we changed our mind and took the option of the best precision.
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    */
         fprintf(ficrespij,"******\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
          
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    agelim=AGESUP;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    /* If stepm=6 months */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           oldm=oldms;savm=savms;      
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    /* nhstepm age range expressed in number of stepm */
           fprintf(ficrespij,"# Age");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
           for(i=1; i<=nlstate;i++)    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
             for(j=1; j<=nlstate+ndeath;j++)    /* if (stepm >= YEARM) hstepm=1;*/
               fprintf(ficrespij," %1d-%1d",i,j);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           fprintf(ficrespij,"\n");    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    for (age=bage; age<=fage; age ++){ 
             for(i=1; i<=nlstate;i++)      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
               for(j=1; j<=nlstate+ndeath;j++)      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      /* if (stepm >= YEARM) hstepm=1;*/
             fprintf(ficrespij,"\n");      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* If stepm=6 months */
           fprintf(ficrespij,"\n");      /* Computed by stepm unit matrices, product of hstepma matrices, stored
         }         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     }      
   }      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       
   fclose(ficrespij);      printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   if(stepm == 1) {      
   /*---------- Forecasting ------------------*/      /* Computing expectancies */
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
   /*printf("calage= %f", calagedate);*/          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;
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            
             /* 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]);*/
   
   strcpy(fileresf,"f");          }
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {      fprintf(ficreseij,"%3.0f",age );
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;      for(i=1; i<=nlstate;i++){
   }        eip=0;
   printf("Computing forecasting: result on file '%s' \n", fileresf);        for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
   free_matrix(mint,1,maxwav,1,n);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   free_matrix(anint,1,maxwav,1,n);        }
   free_matrix(agev,1,maxwav,1,imx);        fprintf(ficreseij,"%9.4f", eip );
   /* Mobile average */      }
       fprintf(ficreseij,"\n");
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      
     }
   if (mobilav==1) {    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    printf("\n");
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)    fprintf(ficlog,"\n");
       for (i=1; i<=nlstate;i++)    
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  }
           mobaverage[(int)agedeb][i][cptcod]=0.;  
      void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
     for (agedeb=bage+4; agedeb<=fage; agedeb++){  
       for (i=1; i<=nlstate;i++){  {
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    /* Covariances of health expectancies eij and of total life expectancies according
           for (cpt=0;cpt<=4;cpt++){     to initial status i, ei. .
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    */
           }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    int nhstepma, nstepma; /* Decreasing with age */
         }    double age, agelim, hf;
       }    double ***p3matp, ***p3matm, ***varhe;
     }      double **dnewm,**doldm;
   }    double *xp, *xm;
     double **gp, **gm;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double ***gradg, ***trgradg;
   if (stepm<=12) stepsize=1;    int theta;
   
   agelim=AGESUP;    double eip, vip;
   /*hstepm=stepsize*YEARM; *//* Every year of age */  
   hstepm=1;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */    xp=vector(1,npar);
   yp1=modf(dateintmean,&yp);    xm=vector(1,npar);
   anprojmean=yp;    dnewm=matrix(1,nlstate*nlstate,1,npar);
   yp2=modf((yp1*12),&yp);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   mprojmean=yp;    
   yp1=modf((yp2*30.5),&yp);    pstamp(ficresstdeij);
   jprojmean=yp;    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   if(jprojmean==0) jprojmean=1;    fprintf(ficresstdeij,"# Age");
   if(mprojmean==0) jprojmean=1;    for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
   if (popforecast==1) {    }
     if((ficpop=fopen(popfile,"r"))==NULL)    {    fprintf(ficresstdeij,"\n");
       printf("Problem with population file : %s\n",popfile);goto end;  
     }    pstamp(ficrescveij);
     popage=ivector(0,AGESUP);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     popeffectif=vector(0,AGESUP);    fprintf(ficrescveij,"# Age");
     popcount=vector(0,AGESUP);    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
     i=1;          cptj= (j-1)*nlstate+i;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)        for(i2=1; i2<=nlstate;i2++)
       {          for(j2=1; j2<=nlstate;j2++){
         i=i+1;            cptj2= (j2-1)*nlstate+i2;
       }            if(cptj2 <= cptj)
     imx=i;              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
              }
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      }
   }    fprintf(ficrescveij,"\n");
     
   for(cptcov=1;cptcov<=i1;cptcov++){    if(estepm < stepm){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      printf ("Problem %d lower than %d\n",estepm, stepm);
       k=k+1;    }
       fprintf(ficresf,"\n#******");    else  hstepm=estepm;   
       for(j=1;j<=cptcoveff;j++) {    /* We compute the life expectancy from trapezoids spaced every estepm months
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     * This is mainly to measure the difference between two models: for example
       }     * if stepm=24 months pijx are given only every 2 years and by summing them
       fprintf(ficresf,"******\n");     * we are calculating an estimate of the Life Expectancy assuming a linear 
       fprintf(ficresf,"# StartingAge FinalAge");     * progression in between and thus overestimating or underestimating according
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);     * to the curvature of the survival function. If, for the same date, we 
       if (popforecast==1)  fprintf(ficresf," [Population]");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         * to compare the new estimate of Life expectancy with the same linear 
       for (cpt=0; cpt<4;cpt++) {     * hypothesis. A more precise result, taking into account a more precise
         fprintf(ficresf,"\n");     * curvature will be obtained if estepm is as small as stepm. */
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
     /* For example we decided to compute the life expectancy with the smallest unit */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       nhstepm is the number of hstepm from age to agelim 
         nhstepm = nhstepm/hstepm;       nstepm is the number of stepm from age to agelin. 
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         oldm=oldms;savm=savms;       survival function given by stepm (the optimization length). Unfortunately it
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         means that if the survival funtion is printed only each two years of age and if
               you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         for (h=0; h<=nhstepm; h++){       results. So we changed our mind and took the option of the best precision.
           if (h==(int) (calagedate+YEARM*cpt)) {    */
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           }  
           for(j=1; j<=nlstate+ndeath;j++) {    /* If stepm=6 months */
             kk1=0.;kk2=0;    /* nhstepm age range expressed in number of stepm */
             for(i=1; i<=nlstate;i++) {            agelim=AGESUP;
               if (mobilav==1)    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
               else {    /* if (stepm >= YEARM) hstepm=1;*/
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/    
               }    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
             }    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
              gp=matrix(0,nhstepm,1,nlstate*nlstate);
             if (h==(int)(calagedate+12*cpt)){    gm=matrix(0,nhstepm,1,nlstate*nlstate);
               fprintf(ficresf," %.3f", kk1);  
                  for (age=bage; age<=fage; age ++){ 
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
             }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           }      /* if (stepm >= YEARM) hstepm=1;*/
         }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
       }      /* If stepm=6 months */
       }      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     }         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   }      
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if (popforecast==1) {  
     free_ivector(popage,0,AGESUP);      /* Computing  Variances of health expectancies */
     free_vector(popeffectif,0,AGESUP);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     free_vector(popcount,0,AGESUP);         decrease memory allocation */
   }      for(theta=1; theta <=npar; theta++){
   free_imatrix(s,1,maxwav+1,1,n);        for(i=1; i<=npar; i++){ 
   free_vector(weight,1,n);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   fclose(ficresf);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
   }/* End forecasting */        }
   else{        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
     erreur=108;        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);    
   }        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
   /*---------- Health expectancies and variances ------------*/            for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
   strcpy(filerest,"t");              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
   strcat(filerest,fileres);            }
   if((ficrest=fopen(filerest,"w"))==NULL) {          }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        }
   }       
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
   strcpy(filerese,"e");          }
   strcat(filerese,fileres);      }/* End theta */
   if((ficreseij=fopen(filerese,"w"))==NULL) {      
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      
   }      for(h=0; h<=nhstepm-1; h++)
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
  strcpy(fileresv,"v");            trgradg[h][j][theta]=gradg[h][theta][j];
   strcat(fileresv,fileres);      
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);       for(ij=1;ij<=nlstate*nlstate;ij++)
   }        for(ji=1;ji<=nlstate*nlstate;ji++)
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          varhe[ij][ji][(int)age] =0.;
   
   k=0;       printf("%d|",(int)age);fflush(stdout);
   for(cptcov=1;cptcov<=i1;cptcov++){       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       for(h=0;h<=nhstepm-1;h++){
       k=k+1;        for(k=0;k<=nhstepm-1;k++){
       fprintf(ficrest,"\n#****** ");          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       for(j=1;j<=cptcoveff;j++)          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(ij=1;ij<=nlstate*nlstate;ij++)
       fprintf(ficrest,"******\n");            for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       fprintf(ficreseij,"\n#****** ");        }
       for(j=1;j<=cptcoveff;j++)      }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");      /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       fprintf(ficresvij,"\n#****** ");      for(i=1; i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++)        for(j=1; j<=nlstate;j++)
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       fprintf(ficresvij,"******\n");            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            /* 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]);*/
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);            }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;      fprintf(ficresstdeij,"%3.0f",age );
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      for(i=1; i<=nlstate;i++){
              eip=0.;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        vip=0.;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        for(j=1; j<=nlstate;j++){
       fprintf(ficrest,"\n");          eip += eij[i][j][(int)age];
                  for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
       hf=1;            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
       if (stepm >= YEARM) hf=stepm/YEARM;          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
       epj=vector(1,nlstate+1);        }
       for(age=bage; age <=fage ;age++){        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      }
         if (popbased==1) {      fprintf(ficresstdeij,"\n");
           for(i=1; i<=nlstate;i++)  
             prlim[i][i]=probs[(int)age][i][k];      fprintf(ficrescveij,"%3.0f",age );
         }      for(i=1; i<=nlstate;i++)
                for(j=1; j<=nlstate;j++){
         fprintf(ficrest," %.0f",age);          cptj= (j-1)*nlstate+i;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          for(i2=1; i2<=nlstate;i2++)
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            for(j2=1; j2<=nlstate;j2++){
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];              cptj2= (j2-1)*nlstate+i2;
           }              if(cptj2 <= cptj)
           epj[nlstate+1] +=epj[j];                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
         }            }
         for(i=1, vepp=0.;i <=nlstate;i++)        }
           for(j=1;j <=nlstate;j++)      fprintf(ficrescveij,"\n");
             vepp += vareij[i][j][(int)age];     
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    }
         for(j=1;j <=nlstate;j++){    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
         }    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
         fprintf(ficrest,"\n");    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       }    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }    printf("\n");
            fprintf(ficlog,"\n");
          
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
  fclose(ficreseij);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
  fclose(ficresvij);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   fclose(ficrest);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   fclose(ficpar);  }
   free_vector(epj,1,nlstate+1);  
   /*  scanf("%d ",i); */  /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   /*------- Variance limit prevalence------*/    {
     /* Variance of health expectancies */
 strcpy(fileresvpl,"vpl");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   strcat(fileresvpl,fileres);    /* double **newm;*/
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    double **dnewm,**doldm;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    double **dnewmp,**doldmp;
     exit(0);    int i, j, nhstepm, hstepm, h, nstepm ;
   }    int k, cptcode;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    double *xp;
     double **gp, **gm;  /* for var eij */
  k=0;    double ***gradg, ***trgradg; /*for var eij */
  for(cptcov=1;cptcov<=i1;cptcov++){    double **gradgp, **trgradgp; /* for var p point j */
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double *gpp, *gmp; /* for var p point j */
      k=k+1;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
      fprintf(ficresvpl,"\n#****** ");    double ***p3mat;
      for(j=1;j<=cptcoveff;j++)    double age,agelim, hf;
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double ***mobaverage;
      fprintf(ficresvpl,"******\n");    int theta;
          char digit[4];
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    char digitp[25];
      oldm=oldms;savm=savms;  
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    char fileresprobmorprev[FILENAMELENGTH];
    }  
  }    if(popbased==1){
       if(mobilav!=0)
   fclose(ficresvpl);        strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
   /*---------- End : free ----------------*/    }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    else 
        strcpy(digitp,"-stablbased-");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    if (mobilav!=0) {
        mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      }
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    }
    
   free_matrix(matcov,1,npar,1,npar);    strcpy(fileresprobmorprev,"prmorprev"); 
   free_vector(delti,1,npar);    sprintf(digit,"%-d",ij);
      /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   if(erreur >0)    strcat(fileresprobmorprev,fileres);
     printf("End of Imach with error %d\n",erreur);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   else   printf("End of Imach\n");      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
      }
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   /*printf("Total time was %d uSec.\n", total_usecs);*/   
   /*------ End -----------*/    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);
  end:    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
 #ifdef windows    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   /* chdir(pathcd);*/      fprintf(ficresprobmorprev," p.%-d SE",j);
 #endif      for(i=1; i<=nlstate;i++)
  /*system("wgnuplot graph.plt");*/        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
  /*system("../gp37mgw/wgnuplot graph.plt");*/    }  
  /*system("cd ../gp37mgw");*/    fprintf(ficresprobmorprev,"\n");
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    fprintf(ficgp,"\n# Routine varevsij");
  strcpy(plotcmd,GNUPLOTPROGRAM);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
  strcat(plotcmd," ");    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");
  strcat(plotcmd,optionfilegnuplot);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
  system(plotcmd);  /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 #ifdef windows    pstamp(ficresvij);
   while (z[0] != 'q') {    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     chdir(path);    if(popbased==1)
     printf("\nType e to edit output files, c to start again, and q for exiting: ");      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);
     scanf("%s",z);    else
     if (z[0] == 'c') system("./imach");      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     else if (z[0] == 'e') {    fprintf(ficresvij,"# Age");
       chdir(path);    for(i=1; i<=nlstate;i++)
       system(optionfilehtm);      for(j=1; j<=nlstate;j++)
     }        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     else if (z[0] == 'q') exit(0);    fprintf(ficresvij,"\n");
   }  
 #endif    xp=vector(1,npar);
 }    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **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>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">",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 : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,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*/
     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*/
     
     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 (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         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] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    avoid:
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int i1, j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       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.1.22  
changed lines
  Added in v.1.146


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