Diff for /imach/src/imach.c between versions 1.44 and 1.150

version 1.44, 2002/05/24 13:01:48 version 1.150, 2014/06/18 16:42:35
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.150  2014/06/18 16:42:35  brouard
      Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
   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    Revision 1.149  2014/06/18 15:51:14  brouard
   interviewed on their health status or degree of disability (in the    Summary: Some fixes in parameter files errors
   case of a health survey which is our main interest) -2- at least a    Author: Nicolas Brouard
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.148  2014/06/17 17:38:48  brouard
   computed from the time spent in each health state according to a    Summary: Nothing new
   model. More health states you consider, more time is necessary to reach the    Author: Brouard
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Just a new packaging for OS/X version 0.98nS
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.147  2014/06/16 10:33:11  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    *** empty log message ***
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.146  2014/06/16 10:20:28  brouard
   where the markup *Covariates have to be included here again* invites    Summary: Merge
   you to do it.  More covariates you add, slower the    Author: Brouard
   convergence.  
     Merge, before building revised version.
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.145  2014/06/10 21:23:15  brouard
   identical for each individual. Also, if a individual missed an    Summary: Debugging with valgrind
   intermediate interview, the information is lost, but taken into    Author: Nicolas Brouard
   account using an interpolation or extrapolation.    
     Lot of changes in order to output the results with some covariates
   hPijx is the probability to be observed in state i at age x+h    After the Edimburgh REVES conference 2014, it seems mandatory to
   conditional to the observed state i at age x. The delay 'h' can be    improve the code.
   split into an exact number (nh*stepm) of unobserved intermediate    No more memory valgrind error but a lot has to be done in order to
   states. This elementary transition (by month or quarter trimester,    continue the work of splitting the code into subroutines.
   semester or year) is model as a multinomial logistic.  The hPx    Also, decodemodel has been improved. Tricode is still not
   matrix is simply the matrix product of nh*stepm elementary matrices    optimal. nbcode should be improved. Documentation has been added in
   and the contribution of each individual to the likelihood is simply    the source code.
   hPijx.  
     Revision 1.143  2014/01/26 09:45:38  brouard
   Also this programme outputs the covariance matrix of the parameters but also    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   of the life expectancies. It also computes the prevalence limits.  
      * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.142  2014/01/26 03:57:36  brouard
   from the European Union.    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.141  2014/01/26 02:42:01  brouard
      * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #include <math.h>  
 #include <stdio.h>    Revision 1.140  2011/09/02 10:37:54  brouard
 #include <stdlib.h>    Summary: times.h is ok with mingw32 now.
 #include <unistd.h>  
     Revision 1.139  2010/06/14 07:50:17  brouard
 #define MAXLINE 256    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 #define GNUPLOTPROGRAM "gnuplot"    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.138  2010/04/30 18:19:40  brouard
 /*#define DEBUG*/    *** empty log message ***
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.137  2010/04/29 18:11:38  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    (Module): Checking covariates for more complex models
     than V1+V2. A lot of change to be done. Unstable.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.136  2010/04/26 20:30:53  brouard
     (Module): merging some libgsl code. Fixing computation
 #define NINTERVMAX 8    of likelione (using inter/intrapolation if mle = 0) in order to
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    get same likelihood as if mle=1.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Some cleaning of code and comments added.
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.135  2009/10/29 15:33:14  brouard
 #define YEARM 12. /* Number of months per year */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.134  2009/10/29 13:18:53  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
 int erreur; /* Error number */    Revision 1.133  2009/07/06 10:21:25  brouard
 int nvar;    just nforces
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.132  2009/07/06 08:22:05  brouard
 int nlstate=2; /* Number of live states */    Many tings
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.131  2009/06/20 16:22:47  brouard
 int popbased=0;    Some dimensions resccaled
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.130  2009/05/26 06:44:34  brouard
 int maxwav; /* Maxim number of waves */    (Module): Max Covariate is now set to 20 instead of 8. A
 int jmin, jmax; /* min, max spacing between 2 waves */    lot of cleaning with variables initialized to 0. Trying to make
 int mle, weightopt;    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.129  2007/08/31 13:49:27  lievre
 double jmean; /* Mean space between 2 waves */    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.128  2006/06/30 13:02:05  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    (Module): Clarifications on computing e.j
 FILE *ficgp,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.127  2006/04/28 18:11:50  brouard
   char filerese[FILENAMELENGTH];    (Module): Yes the sum of survivors was wrong since
  FILE  *ficresvij;    imach-114 because nhstepm was no more computed in the age
   char fileresv[FILENAMELENGTH];    loop. Now we define nhstepma in the age loop.
  FILE  *ficresvpl;    (Module): In order to speed up (in case of numerous covariates) we
   char fileresvpl[FILENAMELENGTH];    compute health expectancies (without variances) in a first step
     and then all the health expectancies with variances or standard
 #define NR_END 1    deviation (needs data from the Hessian matrices) which slows the
 #define FREE_ARG char*    computation.
 #define FTOL 1.0e-10    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
 #define NRANSI  
 #define ITMAX 200    Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
 #define TOL 2.0e-4    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
 #define CGOLD 0.3819660    Version 0.98h
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
 #define GOLD 1.618034    Forecasting file added.
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.124  2006/03/22 17:13:53  lievre
     Parameters are printed with %lf instead of %f (more numbers after the comma).
 static double maxarg1,maxarg2;    The log-likelihood is printed in the log file
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.123  2006/03/20 10:52:43  brouard
      * imach.c (Module): <title> changed, corresponds to .htm file
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    name. <head> headers where missing.
 #define rint(a) floor(a+0.5)  
     * imach.c (Module): Weights can have a decimal point as for
 static double sqrarg;    English (a comma might work with a correct LC_NUMERIC environment,
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    otherwise the weight is truncated).
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Modification of warning when the covariates values are not 0 or
     1.
 int imx;    Version 0.98g
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
 int estepm;    English (a comma might work with a correct LC_NUMERIC environment,
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 int m,nb;    1.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Version 0.98g
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.121  2006/03/16 17:45:01  lievre
 double dateintmean=0;    * imach.c (Module): Comments concerning covariates added
   
 double *weight;    * imach.c (Module): refinements in the computation of lli if
 int **s; /* Status */    status=-2 in order to have more reliable computation if stepm is
 double *agedc, **covar, idx;    not 1 month. Version 0.98f
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.120  2006/03/16 15:10:38  lievre
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): refinements in the computation of lli if
 double ftolhess; /* Tolerance for computing hessian */    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.119  2006/03/15 17:42:26  brouard
 {    (Module): Bug if status = -2, the loglikelihood was
    char *s;                             /* pointer */    computed as likelihood omitting the logarithm. Version O.98e
    int  l1, l2;                         /* length counters */  
     Revision 1.118  2006/03/14 18:20:07  brouard
    l1 = strlen( path );                 /* length of path */    (Module): varevsij Comments added explaining the second
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    table of variances if popbased=1 .
 #ifdef windows    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    s = strrchr( path, '\\' );           /* find last / */    (Module): Function pstamp added
 #else    (Module): Version 0.98d
    s = strrchr( path, '/' );            /* find last / */  
 #endif    Revision 1.117  2006/03/14 17:16:22  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    (Module): varevsij Comments added explaining the second
 #if     defined(__bsd__)                /* get current working directory */    table of variances if popbased=1 .
       extern char       *getwd( );    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
       if ( getwd( dirc ) == NULL ) {    (Module): Version 0.98d
 #else  
       extern char       *getcwd( );    Revision 1.116  2006/03/06 10:29:27  brouard
     (Module): Variance-covariance wrong links and
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    varian-covariance of ej. is needed (Saito).
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.115  2006/02/27 12:17:45  brouard
       }    (Module): One freematrix added in mlikeli! 0.98c
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.114  2006/02/26 12:57:58  brouard
       s++;                              /* after this, the filename */    (Module): Some improvements in processing parameter
       l2 = strlen( s );                 /* length of filename */    filename with strsep.
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.113  2006/02/24 14:20:24  brouard
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    (Module): Memory leaks checks with valgrind and:
       dirc[l1-l2] = 0;                  /* add zero */    datafile was not closed, some imatrix were not freed and on matrix
    }    allocation too.
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    Revision 1.112  2006/01/30 09:55:26  brouard
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Revision 1.111  2006/01/25 20:38:18  brouard
 #endif    (Module): Lots of cleaning and bugs added (Gompertz)
    s = strrchr( name, '.' );            /* find last / */    (Module): Comments can be added in data file. Missing date values
    s++;    can be a simple dot '.'.
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Revision 1.110  2006/01/25 00:51:50  brouard
    l2= strlen( s)+1;    (Module): Lots of cleaning and bugs added (Gompertz)
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.109  2006/01/24 19:37:15  brouard
    return( 0 );                         /* we're done */    (Module): Comments (lines starting with a #) are allowed in data.
 }  
     Revision 1.108  2006/01/19 18:05:42  lievre
     Gnuplot problem appeared...
 /******************************************/    To be fixed
   
 void replace(char *s, char*t)    Revision 1.107  2006/01/19 16:20:37  brouard
 {    Test existence of gnuplot in imach path
   int i;  
   int lg=20;    Revision 1.106  2006/01/19 13:24:36  brouard
   i=0;    Some cleaning and links added in html output
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.105  2006/01/05 20:23:19  lievre
     (s[i] = t[i]);    *** empty log message ***
     if (t[i]== '\\') s[i]='/';  
   }    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
 int nbocc(char *s, char occ)    that the person is alive, then we can code his/her status as -2
 {    (instead of missing=-1 in earlier versions) and his/her
   int i,j=0;    contributions to the likelihood is 1 - Prob of dying from last
   int lg=20;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   i=0;    the healthy state at last known wave). Version is 0.98
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.103  2005/09/30 15:54:49  lievre
   if  (s[i] == occ ) j++;    (Module): sump fixed, loop imx fixed, and simplifications.
   }  
   return j;    Revision 1.102  2004/09/15 17:31:30  brouard
 }    Add the possibility to read data file including tab characters.
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.101  2004/09/15 10:38:38  brouard
 {    Fix on curr_time
   int i,lg,j,p=0;  
   i=0;    Revision 1.100  2004/07/12 18:29:06  brouard
   for(j=0; j<=strlen(t)-1; j++) {    Add version for Mac OS X. Just define UNIX in Makefile
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
   lg=strlen(t);  
   for(j=0; j<p; j++) {    Revision 1.98  2004/05/16 15:05:56  brouard
     (u[j] = t[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
      u[p]='\0';    state at each age, but using a Gompertz model: log u =a + b*age .
     This is the basic analysis of mortality and should be done before any
    for(j=0; j<= lg; j++) {    other analysis, in order to test if the mortality estimated from the
     if (j>=(p+1))(v[j-p-1] = t[j]);    cross-longitudinal survey is different from the mortality estimated
   }    from other sources like vital statistic data.
 }  
     The same imach parameter file can be used but the option for mle should be -3.
 /********************** nrerror ********************/  
     Agnès, who wrote this part of the code, tried to keep most of the
 void nrerror(char error_text[])    former routines in order to include the new code within the former code.
 {  
   fprintf(stderr,"ERREUR ...\n");    The output is very simple: only an estimate of the intercept and of
   fprintf(stderr,"%s\n",error_text);    the slope with 95% confident intervals.
   exit(1);  
 }    Current limitations:
 /*********************** vector *******************/    A) Even if you enter covariates, i.e. with the
 double *vector(int nl, int nh)    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.
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.97  2004/02/20 13:25:42  lievre
   if (!v) nrerror("allocation failure in vector");    Version 0.96d. Population forecasting command line is (temporarily)
   return v-nl+NR_END;    suppressed.
 }  
     Revision 1.96  2003/07/15 15:38:55  brouard
 /************************ free vector ******************/    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 void free_vector(double*v, int nl, int nh)    rewritten within the same printf. Workaround: many printfs.
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.95  2003/07/08 07:54:34  brouard
 }    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 /************************ivector *******************************/    matrix (cov(a12,c31) instead of numbers.
 int *ivector(long nl,long nh)  
 {    Revision 1.94  2003/06/27 13:00:02  brouard
   int *v;    Just cleaning
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    Revision 1.93  2003/06/25 16:33:55  brouard
   return v-nl+NR_END;    (Module): On windows (cygwin) function asctime_r doesn't
 }    exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    Revision 1.92  2003/06/25 16:30:45  brouard
 {    (Module): On windows (cygwin) function asctime_r doesn't
   free((FREE_ARG)(v+nl-NR_END));    exist so I changed back to asctime which exists.
 }  
     Revision 1.91  2003/06/25 15:30:29  brouard
 /******************* imatrix *******************************/    * imach.c (Repository): Duplicated warning errors corrected.
 int **imatrix(long nrl, long nrh, long ncl, long nch)    (Repository): Elapsed time after each iteration is now output. It
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    helps to forecast when convergence will be reached. Elapsed time
 {    is stamped in powell.  We created a new html file for the graphs
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    concerning matrix of covariance. It has extension -cov.htm.
   int **m;  
      Revision 1.90  2003/06/24 12:34:15  brouard
   /* allocate pointers to rows */    (Module): Some bugs corrected for windows. Also, when
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    mle=-1 a template is output in file "or"mypar.txt with the design
   if (!m) nrerror("allocation failure 1 in matrix()");    of the covariance matrix to be input.
   m += NR_END;  
   m -= nrl;    Revision 1.89  2003/06/24 12:30:52  brouard
      (Module): Some bugs corrected for windows. Also, when
      mle=-1 a template is output in file "or"mypar.txt with the design
   /* allocate rows and set pointers to them */    of the covariance matrix to be input.
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.88  2003/06/23 17:54:56  brouard
   m[nrl] += NR_END;    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   m[nrl] -= ncl;  
      Revision 1.87  2003/06/18 12:26:01  brouard
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    Version 0.96
    
   /* return pointer to array of pointers to rows */    Revision 1.86  2003/06/17 20:04:08  brouard
   return m;    (Module): Change position of html and gnuplot routines and added
 }    routine fileappend.
   
 /****************** free_imatrix *************************/    Revision 1.85  2003/06/17 13:12:43  brouard
 void free_imatrix(m,nrl,nrh,ncl,nch)    * imach.c (Repository): Check when date of death was earlier that
       int **m;    current date of interview. It may happen when the death was just
       long nch,ncl,nrh,nrl;    prior to the death. In this case, dh was negative and likelihood
      /* free an int matrix allocated by imatrix() */    was wrong (infinity). We still send an "Error" but patch by
 {    assuming that the date of death was just one stepm after the
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    interview.
   free((FREE_ARG) (m+nrl-NR_END));    (Repository): Because some people have very long ID (first column)
 }    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
 /******************* matrix *******************************/    truncation)
 double **matrix(long nrl, long nrh, long ncl, long nch)    (Repository): No more line truncation errors.
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    Revision 1.84  2003/06/13 21:44:43  brouard
   double **m;    * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    many times. Probs is memory consuming and must be used with
   if (!m) nrerror("allocation failure 1 in matrix()");    parcimony.
   m += NR_END;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   m -= nrl;  
     Revision 1.83  2003/06/10 13:39:11  lievre
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    *** empty log message ***
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.82  2003/06/05 15:57:20  brouard
   m[nrl] -= ncl;    Add log in  imach.c and  fullversion number is now printed.
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  */
   return m;  /*
 }     Interpolated Markov Chain
   
 /*************************free matrix ************************/    Short summary of the programme:
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    
 {    This program computes Healthy Life Expectancies from
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   free((FREE_ARG)(m+nrl-NR_END));    first survey ("cross") where individuals from different ages are
 }    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
 /******************* ma3x *******************************/    second wave of interviews ("longitudinal") which measure each change
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    (if any) in individual health status.  Health expectancies are
 {    computed from the time spent in each health state according to a
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    model. More health states you consider, more time is necessary to reach the
   double ***m;    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    probability to be observed in state j at the second wave
   if (!m) nrerror("allocation failure 1 in matrix()");    conditional to be observed in state i at the first wave. Therefore
   m += NR_END;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   m -= nrl;    'age' is age and 'sex' is a covariate. If you want to have a more
     complex model than "constant and age", you should modify the program
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    where the markup *Covariates have to be included here again* invites
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    you to do it.  More covariates you add, slower the
   m[nrl] += NR_END;    convergence.
   m[nrl] -= ncl;  
     The advantage of this computer programme, compared to a simple
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    intermediate interview, the information is lost, but taken into
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    account using an interpolation or extrapolation.  
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;    hPijx is the probability to be observed in state i at age x+h
   for (j=ncl+1; j<=nch; j++)    conditional to the observed state i at age x. The delay 'h' can be
     m[nrl][j]=m[nrl][j-1]+nlay;    split into an exact number (nh*stepm) of unobserved intermediate
      states. This elementary transition (by month, quarter,
   for (i=nrl+1; i<=nrh; i++) {    semester or year) is modelled as a multinomial logistic.  The hPx
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    matrix is simply the matrix product of nh*stepm elementary matrices
     for (j=ncl+1; j<=nch; j++)    and the contribution of each individual to the likelihood is simply
       m[i][j]=m[i][j-1]+nlay;    hPijx.
   }  
   return m;    Also this programme outputs the covariance matrix of the parameters but also
 }    of the life expectancies. It also computes the period (stable) prevalence. 
     
 /*************************free ma3x ************************/    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)             Institut national d'études démographiques, Paris.
 {    This software have been partly granted by Euro-REVES, a concerted action
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    from the European Union.
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    It is copyrighted identically to a GNU software product, ie programme and
   free((FREE_ARG)(m+nrl-NR_END));    software can be distributed freely for non commercial use. Latest version
 }    can be accessed at http://euroreves.ined.fr/imach .
   
 /***************** f1dim *************************/    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 extern int ncom;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 extern double *pcom,*xicom;    
 extern double (*nrfunc)(double []);    **********************************************************************/
    /*
 double f1dim(double x)    main
 {    read parameterfile
   int j;    read datafile
   double f;    concatwav
   double *xt;    freqsummary
      if (mle >= 1)
   xt=vector(1,ncom);      mlikeli
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    print results files
   f=(*nrfunc)(xt);    if mle==1 
   free_vector(xt,1,ncom);       computes hessian
   return f;    read end of parameter file: agemin, agemax, bage, fage, estepm
 }        begin-prev-date,...
     open gnuplot file
 /*****************brent *************************/    open html file
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
 {     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   int iter;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
   double a,b,d,etemp;      freexexit2 possible for memory heap.
   double fu,fv,fw,fx;  
   double ftemp;    h Pij x                         | pij_nom  ficrestpij
   double p,q,r,tol1,tol2,u,v,w,x,xm;     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   double e=0.0;         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
           1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   x=w=v=bx;         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   fw=fv=fx=(*f)(x);    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   for (iter=1;iter<=ITMAX;iter++) {     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
     xm=0.5*(a+b);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    forecasting if prevfcast==1 prevforecast call prevalence()
     printf(".");fflush(stdout);    health expectancies
 #ifdef DEBUG    Variance-covariance of DFLE
     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);    prevalence()
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */     movingaverage()
 #endif    varevsij() 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    if popbased==1 varevsij(,popbased)
       *xmin=x;    total life expectancies
       return fx;    Variance of period (stable) prevalence
     }   end
     ftemp=fu;  */
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;   
       q=2.0*(q-r);  #include <math.h>
       if (q > 0.0) p = -p;  #include <stdio.h>
       q=fabs(q);  #include <stdlib.h>
       etemp=e;  #include <string.h>
       e=d;  #include <unistd.h>
       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));  #include <limits.h>
       else {  #include <sys/types.h>
         d=p/q;  #include <sys/stat.h>
         u=x+d;  #include <errno.h>
         if (u-a < tol2 || b-u < tol2)  extern int errno;
           d=SIGN(tol1,xm-x);  
       }  #ifdef LINUX
     } else {  #include <time.h>
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  #include "timeval.h"
     }  #else
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #include <sys/time.h>
     fu=(*f)(u);  #endif
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;  #ifdef GSL
       SHFT(v,w,x,u)  #include <gsl/gsl_errno.h>
         SHFT(fv,fw,fx,fu)  #include <gsl/gsl_multimin.h>
         } else {  #endif
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  /* #include <libintl.h> */
             v=w;  /* #define _(String) gettext (String) */
             w=u;  
             fv=fw;  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  #define GNUPLOTPROGRAM "gnuplot"
             v=u;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
             fv=fu;  #define FILENAMELENGTH 132
           }  
         }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   }  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   nrerror("Too many iterations in brent");  
   *xmin=x;  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
   return fx;  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
 }  
   #define NINTERVMAX 8
 /****************** mnbrak ***********************/  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
   #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
             double (*func)(double))  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
 {  #define MAXN 20000
   double ulim,u,r,q, dum;  #define YEARM 12. /**< Number of months per year */
   double fu;  #define AGESUP 130
    #define AGEBASE 40
   *fa=(*func)(*ax);  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
   *fb=(*func)(*bx);  #ifdef UNIX
   if (*fb > *fa) {  #define DIRSEPARATOR '/'
     SHFT(dum,*ax,*bx,dum)  #define CHARSEPARATOR "/"
       SHFT(dum,*fb,*fa,dum)  #define ODIRSEPARATOR '\\'
       }  #else
   *cx=(*bx)+GOLD*(*bx-*ax);  #define DIRSEPARATOR '\\'
   *fc=(*func)(*cx);  #define CHARSEPARATOR "\\"
   while (*fb > *fc) {  #define ODIRSEPARATOR '/'
     r=(*bx-*ax)*(*fb-*fc);  #endif
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  /* $Id$ */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  /* $State$ */
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {  char version[]="Imach version 0.98nT, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
       fu=(*func)(u);  char fullversion[]="$Revision$ $Date$"; 
     } else if ((*cx-u)*(u-ulim) > 0.0) {  char strstart[80];
       fu=(*func)(u);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       if (fu < *fc) {  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  int nvar=0, nforce=0; /* Number of variables, number of forces */
           SHFT(*fb,*fc,fu,(*func)(u))  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
           }  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
       u=ulim;  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
       fu=(*func)(u);  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
     } else {  int cptcovprodnoage=0; /**< Number of covariate products without age */   
       u=(*cx)+GOLD*(*cx-*bx);  int cptcoveff=0; /* Total number of covariates to vary for printing results */
       fu=(*func)(u);  int cptcov=0; /* Working variable */
     }  int npar=NPARMAX;
     SHFT(*ax,*bx,*cx,u)  int nlstate=2; /* Number of live states */
       SHFT(*fa,*fb,*fc,fu)  int ndeath=1; /* Number of dead states */
       }  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 }  int popbased=0;
   
 /*************** linmin ************************/  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav=0; /* Maxim number of waves */
 int ncom;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
 double *pcom,*xicom;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
 double (*nrfunc)(double []);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
                       to the likelihood and the sum of weights (done by funcone)*/
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  int mle=1, weightopt=0;
 {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   double brent(double ax, double bx, double cx,  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
                double (*f)(double), double tol, double *xmin);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   double f1dim(double x);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  double jmean=1; /* Mean space between 2 waves */
               double *fc, double (*func)(double));  double **matprod2(); /* test */
   int j;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double xx,xmin,bx,ax;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   double fx,fb,fa;  /*FILE *fic ; */ /* Used in readdata only */
    FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   ncom=n;  FILE *ficlog, *ficrespow;
   pcom=vector(1,n);  int globpr=0; /* Global variable for printing or not */
   xicom=vector(1,n);  double fretone; /* Only one call to likelihood */
   nrfunc=func;  long ipmx=0; /* Number of contributions */
   for (j=1;j<=n;j++) {  double sw; /* Sum of weights */
     pcom[j]=p[j];  char filerespow[FILENAMELENGTH];
     xicom[j]=xi[j];  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   }  FILE *ficresilk;
   ax=0.0;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   xx=1.0;  FILE *ficresprobmorprev;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  FILE *fichtm, *fichtmcov; /* Html File */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  FILE *ficreseij;
 #ifdef DEBUG  char filerese[FILENAMELENGTH];
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  FILE *ficresstdeij;
 #endif  char fileresstde[FILENAMELENGTH];
   for (j=1;j<=n;j++) {  FILE *ficrescveij;
     xi[j] *= xmin;  char filerescve[FILENAMELENGTH];
     p[j] += xi[j];  FILE  *ficresvij;
   }  char fileresv[FILENAMELENGTH];
   free_vector(xicom,1,n);  FILE  *ficresvpl;
   free_vector(pcom,1,n);  char fileresvpl[FILENAMELENGTH];
 }  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 /*************** powell ************************/  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
             double (*func)(double []))  char command[FILENAMELENGTH];
 {  int  outcmd=0;
   void linmin(double p[], double xi[], int n, double *fret,  
               double (*func)(double []));  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  char filelog[FILENAMELENGTH]; /* Log file */
   double fp,fptt;  char filerest[FILENAMELENGTH];
   double *xits;  char fileregp[FILENAMELENGTH];
   pt=vector(1,n);  char popfile[FILENAMELENGTH];
   ptt=vector(1,n);  
   xit=vector(1,n);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   xits=vector(1,n);  
   *fret=(*func)(p);  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   for (j=1;j<=n;j++) pt[j]=p[j];  struct timezone tzp;
   for (*iter=1;;++(*iter)) {  extern int gettimeofday();
     fp=(*fret);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
     ibig=0;  long time_value;
     del=0.0;  extern long time();
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  char strcurr[80], strfor[80];
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  char *endptr;
     printf("\n");  long lval;
     for (i=1;i<=n;i++) {  double dval;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  #define NR_END 1
 #ifdef DEBUG  #define FREE_ARG char*
       printf("fret=%lf \n",*fret);  #define FTOL 1.0e-10
 #endif  
       printf("%d",i);fflush(stdout);  #define NRANSI 
       linmin(p,xit,n,fret,func);  #define ITMAX 200 
       if (fabs(fptt-(*fret)) > del) {  
         del=fabs(fptt-(*fret));  #define TOL 2.0e-4 
         ibig=i;  
       }  #define CGOLD 0.3819660 
 #ifdef DEBUG  #define ZEPS 1.0e-10 
       printf("%d %.12e",i,(*fret));  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #define GOLD 1.618034 
         printf(" x(%d)=%.12e",j,xit[j]);  #define GLIMIT 100.0 
       }  #define TINY 1.0e-20 
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);  static double maxarg1,maxarg2;
       printf("\n");  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 #endif  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     }    
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #ifdef DEBUG  #define rint(a) floor(a+0.5)
       int k[2],l;  
       k[0]=1;  static double sqrarg;
       k[1]=-1;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       printf("Max: %.12e",(*func)(p));  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       for (j=1;j<=n;j++)  int agegomp= AGEGOMP;
         printf(" %.12e",p[j]);  
       printf("\n");  int imx; 
       for(l=0;l<=1;l++) {  int stepm=1;
         for (j=1;j<=n;j++) {  /* Stepm, step in month: minimum step interpolation*/
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  int estepm;
         }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  int m,nb;
 #endif  long *num;
   int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       free_vector(xit,1,n);  double **pmmij, ***probs;
       free_vector(xits,1,n);  double *ageexmed,*agecens;
       free_vector(ptt,1,n);  double dateintmean=0;
       free_vector(pt,1,n);  
       return;  double *weight;
     }  int **s; /* Status */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  double *agedc;
     for (j=1;j<=n;j++) {  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
       ptt[j]=2.0*p[j]-pt[j];                    * covar=matrix(0,NCOVMAX,1,n); 
       xit[j]=p[j]-pt[j];                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       pt[j]=p[j];  double  idx; 
     }  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
     fptt=(*func)(ptt);  int *Ndum; /** Freq of modality (tricode */
     if (fptt < fp) {  int **codtab; /**< codtab=imatrix(1,100,1,10); */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
       if (t < 0.0) {  double *lsurv, *lpop, *tpop;
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
           xi[j][ibig]=xi[j][n];  double ftolhess; /**< Tolerance for computing hessian */
           xi[j][n]=xit[j];  
         }  /**************** split *************************/
 #ifdef DEBUG  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  {
         for(j=1;j<=n;j++)    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
           printf(" %.12e",xit[j]);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
         printf("\n");    */ 
 #endif    char  *ss;                            /* pointer */
       }    int   l1, l2;                         /* length counters */
     }  
   }    l1 = strlen(path );                   /* length of path */
 }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 /**** Prevalence limit ****************/    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       strcpy( name, path );               /* we got the fullname name because no directory */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      /* get current working directory */
      matrix by transitions matrix until convergence is reached */      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   int i, ii,j,k;        return( GLOCK_ERROR_GETCWD );
   double min, max, maxmin, maxmax,sumnew=0.;      }
   double **matprod2();      /* got dirc from getcwd*/
   double **out, cov[NCOVMAX], **pmij();      printf(" DIRC = %s \n",dirc);
   double **newm;    } else {                              /* strip direcotry from path */
   double agefin, delaymax=50 ; /* Max number of years to converge */      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
   for (ii=1;ii<=nlstate+ndeath;ii++)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     for (j=1;j<=nlstate+ndeath;j++){      strcpy( name, ss );         /* save file name */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     }      dirc[l1-l2] = 0;                    /* add zero */
       printf(" DIRC2 = %s \n",dirc);
    cov[1]=1.;    }
      /* We add a separator at the end of dirc if not exists */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    l1 = strlen( dirc );                  /* length of directory */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    if( dirc[l1-1] != DIRSEPARATOR ){
     newm=savm;      dirc[l1] =  DIRSEPARATOR;
     /* Covariates have to be included here again */      dirc[l1+1] = 0; 
      cov[2]=agefin;      printf(" DIRC3 = %s \n",dirc);
      }
       for (k=1; k<=cptcovn;k++) {    ss = strrchr( name, '.' );            /* find last / */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    if (ss >0){
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/      ss++;
       }      strcpy(ext,ss);                     /* save extension */
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      l1= strlen( name);
       for (k=1; k<=cptcovprod;k++)      l2= strlen(ss)+1;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      strncpy( finame, name, l1-l2);
       finame[l1-l2]= 0;
       /*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]);*/  
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    return( 0 );                          /* we're done */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  }
   
     savm=oldm;  
     oldm=newm;  /******************************************/
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  void replace_back_to_slash(char *s, char*t)
       min=1.;  {
       max=0.;    int i;
       for(i=1; i<=nlstate; i++) {    int lg=0;
         sumnew=0;    i=0;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    lg=strlen(t);
         prlim[i][j]= newm[i][j]/(1-sumnew);    for(i=0; i<= lg; i++) {
         max=FMAX(max,prlim[i][j]);      (s[i] = t[i]);
         min=FMIN(min,prlim[i][j]);      if (t[i]== '\\') s[i]='/';
       }    }
       maxmin=max-min;  }
       maxmax=FMAX(maxmax,maxmin);  
     }  char *trimbb(char *out, char *in)
     if(maxmax < ftolpl){  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
       return prlim;    char *s;
     }    s=out;
   }    while (*in != '\0'){
 }      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         in++;
 /*************** transition probabilities ***************/      }
       *out++ = *in++;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    }
 {    *out='\0';
   double s1, s2;    return s;
   /*double t34;*/  }
   int i,j,j1, nc, ii, jj;  
   char *cutl(char *blocc, char *alocc, char *in, char occ)
     for(i=1; i<= nlstate; i++){  {
     for(j=1; j<i;j++){    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
         /*s2 += param[i][j][nc]*cov[nc];*/       gives blocc="abcdef2ghi" and alocc="j".
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];       If occ is not found blocc is null and alocc is equal to in. Returns blocc
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    */
       }    char *s, *t, *bl;
       ps[i][j]=s2;    t=in;s=in;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    while ((*in != occ) && (*in != '\0')){
     }      *alocc++ = *in++;
     for(j=i+1; j<=nlstate+ndeath;j++){    }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    if( *in == occ){
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      *(alocc)='\0';
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      s=++in;
       }    }
       ps[i][j]=s2;   
     }    if (s == t) {/* occ not found */
   }      *(alocc-(in-s))='\0';
     /*ps[3][2]=1;*/      in=s;
     }
   for(i=1; i<= nlstate; i++){    while ( *in != '\0'){
      s1=0;      *blocc++ = *in++;
     for(j=1; j<i; j++)    }
       s1+=exp(ps[i][j]);  
     for(j=i+1; j<=nlstate+ndeath; j++)    *blocc='\0';
       s1+=exp(ps[i][j]);    return t;
     ps[i][i]=1./(s1+1.);  }
     for(j=1; j<i; j++)  char *cutv(char *blocc, char *alocc, char *in, char occ)
       ps[i][j]= exp(ps[i][j])*ps[i][i];  {
     for(j=i+1; j<=nlstate+ndeath; j++)    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
       ps[i][j]= exp(ps[i][j])*ps[i][i];       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */       gives blocc="abcdef2ghi" and alocc="j".
   } /* end i */       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    char *s, *t;
     for(jj=1; jj<= nlstate+ndeath; jj++){    t=in;s=in;
       ps[ii][jj]=0;    while (*in != '\0'){
       ps[ii][ii]=1;      while( *in == occ){
     }        *blocc++ = *in++;
   }        s=in;
       }
       *blocc++ = *in++;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    }
     for(jj=1; jj<= nlstate+ndeath; jj++){    if (s == t) /* occ not found */
      printf("%lf ",ps[ii][jj]);      *(blocc-(in-s))='\0';
    }    else
     printf("\n ");      *(blocc-(in-s)-1)='\0';
     }    in=s;
     printf("\n ");printf("%lf ",cov[2]);*/    while ( *in != '\0'){
 /*      *alocc++ = *in++;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    }
   goto end;*/  
     return ps;    *alocc='\0';
 }    return s;
   }
 /**************** Product of 2 matrices ******************/  
   int nbocc(char *s, char occ)
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  {
 {    int i,j=0;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    int lg=20;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    i=0;
   /* in, b, out are matrice of pointers which should have been initialized    lg=strlen(s);
      before: only the contents of out is modified. The function returns    for(i=0; i<= lg; i++) {
      a pointer to pointers identical to out */    if  (s[i] == occ ) j++;
   long i, j, k;    }
   for(i=nrl; i<= nrh; i++)    return j;
     for(k=ncolol; k<=ncoloh; k++)  }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];  /* void cutv(char *u,char *v, char*t, char occ) */
   /* { */
   return out;  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
 }  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   /*      gives u="abcdef2ghi" and v="j" *\/ */
   /*   int i,lg,j,p=0; */
 /************* Higher Matrix Product ***************/  /*   i=0; */
   /*   lg=strlen(t); */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  /*   for(j=0; j<=lg-1; j++) { */
 {  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  /*   } */
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  /*   for(j=0; j<p; j++) { */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  /*     (u[j] = 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  /*      u[p]='\0'; */
      included manually here.  
   /*    for(j=0; j<= lg; j++) { */
      */  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /*   } */
   int i, j, d, h, k;  /* } */
   double **out, cov[NCOVMAX];  
   double **newm;  /********************** nrerror ********************/
   
   /* Hstepm could be zero and should return the unit matrix */  void nrerror(char error_text[])
   for (i=1;i<=nlstate+ndeath;i++)  {
     for (j=1;j<=nlstate+ndeath;j++){    fprintf(stderr,"ERREUR ...\n");
       oldm[i][j]=(i==j ? 1.0 : 0.0);    fprintf(stderr,"%s\n",error_text);
       po[i][j][0]=(i==j ? 1.0 : 0.0);    exit(EXIT_FAILURE);
     }  }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /*********************** vector *******************/
   for(h=1; h <=nhstepm; h++){  double *vector(int nl, int nh)
     for(d=1; d <=hstepm; d++){  {
       newm=savm;    double *v;
       /* Covariates have to be included here again */    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       cov[1]=1.;    if (!v) nrerror("allocation failure in vector");
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    return v-nl+NR_END;
       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];  /************************ free vector ******************/
       for (k=1; k<=cptcovprod;k++)  void free_vector(double*v, int nl, int nh)
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  {
     free((FREE_ARG)(v+nl-NR_END));
   }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  /************************ivector *******************************/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  int *ivector(long nl,long nh)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  {
       savm=oldm;    int *v;
       oldm=newm;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     }    if (!v) nrerror("allocation failure in ivector");
     for(i=1; i<=nlstate+ndeath; i++)    return v-nl+NR_END;
       for(j=1;j<=nlstate+ndeath;j++) {  }
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /******************free ivector **************************/
          */  void free_ivector(int *v, long nl, long nh)
       }  {
   } /* end h */    free((FREE_ARG)(v+nl-NR_END));
   return po;  }
 }  
   /************************lvector *******************************/
   long *lvector(long nl,long nh)
 /*************** log-likelihood *************/  {
 double func( double *x)    long *v;
 {    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   int i, ii, j, k, mi, d, kk;    if (!v) nrerror("allocation failure in ivector");
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    return v-nl+NR_END;
   double **out;  }
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */  /******************free lvector **************************/
   long ipmx;  void free_lvector(long *v, long nl, long nh)
   /*extern weight */  {
   /* We are differentiating ll according to initial status */    free((FREE_ARG)(v+nl-NR_END));
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  }
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);  /******************* imatrix *******************************/
   */  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   cov[1]=1.;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   { 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    int **m; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    
     for(mi=1; mi<= wav[i]-1; mi++){    /* allocate pointers to rows */ 
       for (ii=1;ii<=nlstate+ndeath;ii++)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    if (!m) nrerror("allocation failure 1 in matrix()"); 
       for(d=0; d<dh[mi][i]; d++){    m += NR_END; 
         newm=savm;    m -= nrl; 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    
         for (kk=1; kk<=cptcovage;kk++) {    
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    /* allocate rows and set pointers to them */ 
         }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
            if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    m[nrl] += NR_END; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    m[nrl] -= ncl; 
         savm=oldm;    
         oldm=newm;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
            
            /* return pointer to array of pointers to rows */ 
       } /* end mult */    return m; 
        } 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  /****************** free_imatrix *************************/
       ipmx +=1;  void free_imatrix(m,nrl,nrh,ncl,nch)
       sw += weight[i];        int **m;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        long nch,ncl,nrh,nrl; 
     } /* end of wave */       /* free an int matrix allocated by imatrix() */ 
   } /* end of individual */  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    free((FREE_ARG) (m+nrl-NR_END)); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  } 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  
   return -l;  /******************* matrix *******************************/
 }  double **matrix(long nrl, long nrh, long ncl, long nch)
   {
     long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 /*********** Maximum Likelihood Estimation ***************/    double **m;
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 {    if (!m) nrerror("allocation failure 1 in matrix()");
   int i,j, iter;    m += NR_END;
   double **xi,*delti;    m -= nrl;
   double fret;  
   xi=matrix(1,npar,1,npar);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   for (i=1;i<=npar;i++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for (j=1;j<=npar;j++)    m[nrl] += NR_END;
       xi[i][j]=(i==j ? 1.0 : 0.0);    m[nrl] -= ncl;
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
 }     */
   }
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /*************************free matrix ************************/
 {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double  **a,**y,*x,pd;  {
   double **hess;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   int i, j,jk;    free((FREE_ARG)(m+nrl-NR_END));
   int *indx;  }
   
   double hessii(double p[], double delta, int theta, double delti[]);  /******************* ma3x *******************************/
   double hessij(double p[], double delti[], int i, int j);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   void lubksb(double **a, int npar, int *indx, double b[]) ;  {
   void ludcmp(double **a, int npar, int *indx, double *d) ;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
   hess=matrix(1,npar,1,npar);  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   printf("\nCalculation of the hessian matrix. Wait...\n");    if (!m) nrerror("allocation failure 1 in matrix()");
   for (i=1;i<=npar;i++){    m += NR_END;
     printf("%d",i);fflush(stdout);    m -= nrl;
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     /*printf(" %lf ",hess[i][i]);*/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   }    m[nrl] += NR_END;
      m[nrl] -= ncl;
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++)  {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         hess[i][j]=hessij(p,delti,i,j);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         hess[j][i]=hess[i][j];        m[nrl][ncl] += NR_END;
         /*printf(" %lf ",hess[i][j]);*/    m[nrl][ncl] -= nll;
       }    for (j=ncl+1; j<=nch; j++) 
     }      m[nrl][j]=m[nrl][j-1]+nlay;
   }    
   printf("\n");    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      for (j=ncl+1; j<=nch; j++) 
          m[i][j]=m[i][j-1]+nlay;
   a=matrix(1,npar,1,npar);    }
   y=matrix(1,npar,1,npar);    return m; 
   x=vector(1,npar);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   indx=ivector(1,npar);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   for (i=1;i<=npar;i++)    */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  }
   ludcmp(a,npar,indx,&pd);  
   /*************************free ma3x ************************/
   for (j=1;j<=npar;j++) {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     for (i=1;i<=npar;i++) x[i]=0;  {
     x[j]=1;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     lubksb(a,npar,indx,x);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     for (i=1;i<=npar;i++){    free((FREE_ARG)(m+nrl-NR_END));
       matcov[i][j]=x[i];  }
     }  
   }  /*************** function subdirf ***********/
   char *subdirf(char fileres[])
   printf("\n#Hessian matrix#\n");  {
   for (i=1;i<=npar;i++) {    /* Caution optionfilefiname is hidden */
     for (j=1;j<=npar;j++) {    strcpy(tmpout,optionfilefiname);
       printf("%.3e ",hess[i][j]);    strcat(tmpout,"/"); /* Add to the right */
     }    strcat(tmpout,fileres);
     printf("\n");    return tmpout;
   }  }
   
   /* Recompute Inverse */  /*************** function subdirf2 ***********/
   for (i=1;i<=npar;i++)  char *subdirf2(char fileres[], char *preop)
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  {
   ludcmp(a,npar,indx,&pd);    
     /* Caution optionfilefiname is hidden */
   /*  printf("\n#Hessian matrix recomputed#\n");    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
   for (j=1;j<=npar;j++) {    strcat(tmpout,preop);
     for (i=1;i<=npar;i++) x[i]=0;    strcat(tmpout,fileres);
     x[j]=1;    return tmpout;
     lubksb(a,npar,indx,x);  }
     for (i=1;i<=npar;i++){  
       y[i][j]=x[i];  /*************** function subdirf3 ***********/
       printf("%.3e ",y[i][j]);  char *subdirf3(char fileres[], char *preop, char *preop2)
     }  {
     printf("\n");    
   }    /* Caution optionfilefiname is hidden */
   */    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
   free_matrix(a,1,npar,1,npar);    strcat(tmpout,preop);
   free_matrix(y,1,npar,1,npar);    strcat(tmpout,preop2);
   free_vector(x,1,npar);    strcat(tmpout,fileres);
   free_ivector(indx,1,npar);    return tmpout;
   free_matrix(hess,1,npar,1,npar);  }
   
   /***************** f1dim *************************/
 }  extern int ncom; 
   extern double *pcom,*xicom;
 /*************** hessian matrix ****************/  extern double (*nrfunc)(double []); 
 double hessii( double x[], double delta, int theta, double delti[])   
 {  double f1dim(double x) 
   int i;  { 
   int l=1, lmax=20;    int j; 
   double k1,k2;    double f;
   double p2[NPARMAX+1];    double *xt; 
   double res;   
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    xt=vector(1,ncom); 
   double fx;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   int k=0,kmax=10;    f=(*nrfunc)(xt); 
   double l1;    free_vector(xt,1,ncom); 
     return f; 
   fx=func(x);  } 
   for (i=1;i<=npar;i++) p2[i]=x[i];  
   for(l=0 ; l <=lmax; l++){  /*****************brent *************************/
     l1=pow(10,l);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     delts=delt;  { 
     for(k=1 ; k <kmax; k=k+1){    int iter; 
       delt = delta*(l1*k);    double a,b,d,etemp;
       p2[theta]=x[theta] +delt;    double fu,fv,fw,fx;
       k1=func(p2)-fx;    double ftemp;
       p2[theta]=x[theta]-delt;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       k2=func(p2)-fx;    double e=0.0; 
       /*res= (k1-2.0*fx+k2)/delt/delt; */   
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    a=(ax < cx ? ax : cx); 
          b=(ax > cx ? ax : cx); 
 #ifdef DEBUG    x=w=v=bx; 
       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);    fw=fv=fx=(*f)(x); 
 #endif    for (iter=1;iter<=ITMAX;iter++) { 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      xm=0.5*(a+b); 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         k=kmax;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       }      printf(".");fflush(stdout);
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      fprintf(ficlog,".");fflush(ficlog);
         k=kmax; l=lmax*10.;  #ifdef DEBUG
       }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      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);
         delts=delt;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       }  #endif
     }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   }        *xmin=x; 
   delti[theta]=delts;        return fx; 
   return res;      } 
        ftemp=fu;
 }      if (fabs(e) > tol1) { 
         r=(x-w)*(fx-fv); 
 double hessij( double x[], double delti[], int thetai,int thetaj)        q=(x-v)*(fx-fw); 
 {        p=(x-v)*q-(x-w)*r; 
   int i;        q=2.0*(q-r); 
   int l=1, l1, lmax=20;        if (q > 0.0) p = -p; 
   double k1,k2,k3,k4,res,fx;        q=fabs(q); 
   double p2[NPARMAX+1];        etemp=e; 
   int k;        e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   fx=func(x);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for (k=1; k<=2; k++) {        else { 
     for (i=1;i<=npar;i++) p2[i]=x[i];          d=p/q; 
     p2[thetai]=x[thetai]+delti[thetai]/k;          u=x+d; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          if (u-a < tol2 || b-u < tol2) 
     k1=func(p2)-fx;            d=SIGN(tol1,xm-x); 
          } 
     p2[thetai]=x[thetai]+delti[thetai]/k;      } else { 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     k2=func(p2)-fx;      } 
        u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     p2[thetai]=x[thetai]-delti[thetai]/k;      fu=(*f)(u); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      if (fu <= fx) { 
     k3=func(p2)-fx;        if (u >= x) a=x; else b=x; 
          SHFT(v,w,x,u) 
     p2[thetai]=x[thetai]-delti[thetai]/k;          SHFT(fv,fw,fx,fu) 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          } else { 
     k4=func(p2)-fx;            if (u < x) a=u; else b=u; 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */            if (fu <= fw || w == x) { 
 #ifdef DEBUG              v=w; 
     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);              w=u; 
 #endif              fv=fw; 
   }              fw=fu; 
   return res;            } else if (fu <= fv || v == x || v == w) { 
 }              v=u; 
               fv=fu; 
 /************** Inverse of matrix **************/            } 
 void ludcmp(double **a, int n, int *indx, double *d)          } 
 {    } 
   int i,imax,j,k;    nrerror("Too many iterations in brent"); 
   double big,dum,sum,temp;    *xmin=x; 
   double *vv;    return fx; 
    } 
   vv=vector(1,n);  
   *d=1.0;  /****************** mnbrak ***********************/
   for (i=1;i<=n;i++) {  
     big=0.0;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     for (j=1;j<=n;j++)              double (*func)(double)) 
       if ((temp=fabs(a[i][j])) > big) big=temp;  { 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    double ulim,u,r,q, dum;
     vv[i]=1.0/big;    double fu; 
   }   
   for (j=1;j<=n;j++) {    *fa=(*func)(*ax); 
     for (i=1;i<j;i++) {    *fb=(*func)(*bx); 
       sum=a[i][j];    if (*fb > *fa) { 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      SHFT(dum,*ax,*bx,dum) 
       a[i][j]=sum;        SHFT(dum,*fb,*fa,dum) 
     }        } 
     big=0.0;    *cx=(*bx)+GOLD*(*bx-*ax); 
     for (i=j;i<=n;i++) {    *fc=(*func)(*cx); 
       sum=a[i][j];    while (*fb > *fc) { 
       for (k=1;k<j;k++)      r=(*bx-*ax)*(*fb-*fc); 
         sum -= a[i][k]*a[k][j];      q=(*bx-*cx)*(*fb-*fa); 
       a[i][j]=sum;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       if ( (dum=vv[i]*fabs(sum)) >= big) {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
         big=dum;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
         imax=i;      if ((*bx-u)*(u-*cx) > 0.0) { 
       }        fu=(*func)(u); 
     }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     if (j != imax) {        fu=(*func)(u); 
       for (k=1;k<=n;k++) {        if (fu < *fc) { 
         dum=a[imax][k];          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         a[imax][k]=a[j][k];            SHFT(*fb,*fc,fu,(*func)(u)) 
         a[j][k]=dum;            } 
       }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       *d = -(*d);        u=ulim; 
       vv[imax]=vv[j];        fu=(*func)(u); 
     }      } else { 
     indx[j]=imax;        u=(*cx)+GOLD*(*cx-*bx); 
     if (a[j][j] == 0.0) a[j][j]=TINY;        fu=(*func)(u); 
     if (j != n) {      } 
       dum=1.0/(a[j][j]);      SHFT(*ax,*bx,*cx,u) 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        SHFT(*fa,*fb,*fc,fu) 
     }        } 
   }  } 
   free_vector(vv,1,n);  /* Doesn't work */  
 ;  /*************** linmin ************************/
 }  
   int ncom; 
 void lubksb(double **a, int n, int *indx, double b[])  double *pcom,*xicom;
 {  double (*nrfunc)(double []); 
   int i,ii=0,ip,j;   
   double sum;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
    { 
   for (i=1;i<=n;i++) {    double brent(double ax, double bx, double cx, 
     ip=indx[i];                 double (*f)(double), double tol, double *xmin); 
     sum=b[ip];    double f1dim(double x); 
     b[ip]=b[i];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     if (ii)                double *fc, double (*func)(double)); 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    int j; 
     else if (sum) ii=i;    double xx,xmin,bx,ax; 
     b[i]=sum;    double fx,fb,fa;
   }   
   for (i=n;i>=1;i--) {    ncom=n; 
     sum=b[i];    pcom=vector(1,n); 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    xicom=vector(1,n); 
     b[i]=sum/a[i][i];    nrfunc=func; 
   }    for (j=1;j<=n;j++) { 
 }      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
 /************ Frequencies ********************/    } 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)    ax=0.0; 
 {  /* Some frequencies */    xx=1.0; 
      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   double ***freq; /* Frequencies */  #ifdef DEBUG
   double *pp;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   double pos, k2, dateintsum=0,k2cpt=0;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   FILE *ficresp;  #endif
   char fileresp[FILENAMELENGTH];    for (j=1;j<=n;j++) { 
        xi[j] *= xmin; 
   pp=vector(1,nlstate);      p[j] += xi[j]; 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    } 
   strcpy(fileresp,"p");    free_vector(xicom,1,n); 
   strcat(fileresp,fileres);    free_vector(pcom,1,n); 
   if((ficresp=fopen(fileresp,"w"))==NULL) {  } 
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     exit(0);  char *asc_diff_time(long time_sec, char ascdiff[])
   }  {
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    long sec_left, days, hours, minutes;
   j1=0;    days = (time_sec) / (60*60*24);
      sec_left = (time_sec) % (60*60*24);
   j=cptcoveff;    hours = (sec_left) / (60*60) ;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    sec_left = (sec_left) %(60*60);
      minutes = (sec_left) /60;
   for(k1=1; k1<=j;k1++){    sec_left = (sec_left) % (60);
     for(i1=1; i1<=ncodemax[k1];i1++){    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
       j1++;    return ascdiff;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  }
         scanf("%d", i);*/  
       for (i=-1; i<=nlstate+ndeath; i++)    /*************** powell ************************/
         for (jk=-1; jk<=nlstate+ndeath; jk++)    void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
           for(m=agemin; m <= agemax+3; m++)              double (*func)(double [])) 
             freq[i][jk][m]=0;  { 
          void linmin(double p[], double xi[], int n, double *fret, 
       dateintsum=0;                double (*func)(double [])); 
       k2cpt=0;    int i,ibig,j; 
       for (i=1; i<=imx; i++) {    double del,t,*pt,*ptt,*xit;
         bool=1;    double fp,fptt;
         if  (cptcovn>0) {    double *xits;
           for (z1=1; z1<=cptcoveff; z1++)    int niterf, itmp;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;    pt=vector(1,n); 
         }    ptt=vector(1,n); 
         if (bool==1) {    xit=vector(1,n); 
           for(m=firstpass; m<=lastpass; m++){    xits=vector(1,n); 
             k2=anint[m][i]+(mint[m][i]/12.);    *fret=(*func)(p); 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    for (j=1;j<=n;j++) pt[j]=p[j]; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;    for (*iter=1;;++(*iter)) { 
               if(agev[m][i]==1) agev[m][i]=agemax+2;      fp=(*fret); 
               if (m<lastpass) {      ibig=0; 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      del=0.0; 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      last_time=curr_time;
               }      (void) gettimeofday(&curr_time,&tzp);
                    printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
                 dateintsum=dateintsum+k2;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
                 k2cpt++;     for (i=1;i<=n;i++) {
               }        printf(" %d %.12f",i, p[i]);
             }        fprintf(ficlog," %d %.12lf",i, p[i]);
           }        fprintf(ficrespow," %.12lf", p[i]);
         }      }
       }      printf("\n");
              fprintf(ficlog,"\n");
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      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");
          #endif
         for(jk=-1; jk <=nlstate+ndeath; jk++)      } 
           for(m=-1; m <=nlstate+ndeath; m++)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  #ifdef DEBUG
         if(i <= (int) agemax)        int k[2],l;
           fprintf(ficresp,"\n");        k[0]=1;
         printf("\n");        k[1]=-1;
       }        printf("Max: %.12e",(*func)(p));
     }        fprintf(ficlog,"Max: %.12e",(*func)(p));
   }        for (j=1;j<=n;j++) {
   dateintmean=dateintsum/k2cpt;          printf(" %.12e",p[j]);
            fprintf(ficlog," %.12e",p[j]);
   fclose(ficresp);        }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        printf("\n");
   free_vector(pp,1,nlstate);        fprintf(ficlog,"\n");
          for(l=0;l<=1;l++) {
   /* End of Freq */          for (j=1;j<=n;j++) {
 }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 /************ Prevalence ********************/            fprintf(ficlog,"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, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)          }
 {  /* Some frequencies */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
            fprintf(ficlog,"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;        }
   double ***freq; /* Frequencies */  #endif
   double *pp;  
   double pos, k2;  
         free_vector(xit,1,n); 
   pp=vector(1,nlstate);        free_vector(xits,1,n); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        free_vector(ptt,1,n); 
          free_vector(pt,1,n); 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        return; 
   j1=0;      } 
        if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   j=cptcoveff;      for (j=1;j<=n;j++) { 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        ptt[j]=2.0*p[j]-pt[j]; 
          xit[j]=p[j]-pt[j]; 
   for(k1=1; k1<=j;k1++){        pt[j]=p[j]; 
     for(i1=1; i1<=ncodemax[k1];i1++){      } 
       j1++;      fptt=(*func)(ptt); 
            if (fptt < fp) { 
       for (i=-1; i<=nlstate+ndeath; i++)          t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         for (jk=-1; jk<=nlstate+ndeath; jk++)          if (t < 0.0) { 
           for(m=agemin; m <= agemax+3; m++)          linmin(p,xit,n,fret,func); 
             freq[i][jk][m]=0;          for (j=1;j<=n;j++) { 
                  xi[j][ibig]=xi[j][n]; 
       for (i=1; i<=imx; i++) {            xi[j][n]=xit[j]; 
         bool=1;          }
         if  (cptcovn>0) {  #ifdef DEBUG
           for (z1=1; z1<=cptcoveff; z1++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
               bool=0;          for(j=1;j<=n;j++){
         }            printf(" %.12e",xit[j]);
         if (bool==1) {            fprintf(ficlog," %.12e",xit[j]);
           for(m=firstpass; m<=lastpass; m++){          }
             k2=anint[m][i]+(mint[m][i]/12.);          printf("\n");
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          fprintf(ficlog,"\n");
               if(agev[m][i]==0) agev[m][i]=agemax+1;  #endif
               if(agev[m][i]==1) agev[m][i]=agemax+2;        }
               if (m<lastpass) {      } 
                 if (calagedate>0)    } 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  } 
                 else  
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  /**** Prevalence limit (stable or period prevalence)  ****************/
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];  
               }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
             }  {
           }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         }       matrix by transitions matrix until convergence is reached */
       }  
       for(i=(int)agemin; i <= (int)agemax+3; i++){    int i, ii,j,k;
         for(jk=1; jk <=nlstate ; jk++){    double min, max, maxmin, maxmax,sumnew=0.;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    /* double **matprod2(); */ /* test */
             pp[jk] += freq[jk][m][i];    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=-1, pos=0; m <=0 ; m++)  
             pos += 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; jk <=nlstate ; jk++){      }
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
             pp[jk] += freq[jk][m][i];     cov[1]=1.;
         }   
           /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
              newm=savm;
         for(jk=1; jk <=nlstate ; jk++){          /* Covariates have to be included here again */
           if( i <= (int) agemax){      cov[2]=agefin;
             if(pos>=1.e-5){      
               probs[i][jk][j1]= pp[jk]/pos;      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]; */
       }      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
     }      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
   }      
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   free_vector(pp,1,nlstate);      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
        /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
 }  /* End of Freq */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
       
 /************* Waves Concatenation ***************/      savm=oldm;
       oldm=newm;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      maxmax=0.;
 {      for(j=1;j<=nlstate;j++){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        min=1.;
      Death is a valid wave (if date is known).        max=0.;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        for(i=1; i<=nlstate; i++) {
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          sumnew=0;
      and mw[mi+1][i]. dh depends on stepm.          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
      */          prlim[i][j]= newm[i][j]/(1-sumnew);
           /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
   int i, mi, m;          max=FMAX(max,prlim[i][j]);
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          min=FMIN(min,prlim[i][j]);
      double sum=0., jmean=0.;*/        }
         maxmin=max-min;
   int j, k=0,jk, ju, jl;        maxmax=FMAX(maxmax,maxmin);
   double sum=0.;      }
   jmin=1e+5;      if(maxmax < ftolpl){
   jmax=-1;        return prlim;
   jmean=0.;      }
   for(i=1; i<=imx; i++){    }
     mi=0;  }
     m=firstpass;  
     while(s[m][i] <= nlstate){  /*************** transition probabilities ***************/ 
       if(s[m][i]>=1)  
         mw[++mi][i]=m;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       if(m >=lastpass)  {
         break;    /* According to parameters values stored in x and the covariate's values stored in cov,
       else       computes the probability to be observed in state j being in state i by appying the
         m++;       model to the ncovmodel covariates (including constant and age).
     }/* end while */       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
     if (s[m][i] > nlstate){       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
       mi++;     /* Death is another wave */       ncth covariate in the global vector x is given by the formula:
       /* if(mi==0)  never been interviewed correctly before death */       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
          /* Only death is a correct wave */       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
       mw[mi][i]=m;       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
     wav[i]=mi;       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     if(mi==0)    */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    double s1, lnpijopii;
   }    /*double t34;*/
     int i,j,j1, nc, ii, jj;
   for(i=1; i<=imx; i++){  
     for(mi=1; mi<wav[i];mi++){      for(i=1; i<= nlstate; i++){
       if (stepm <=0)        for(j=1; j<i;j++){
         dh[mi][i]=1;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       else{            /*lnpijopii += param[i][j][nc]*cov[nc];*/
         if (s[mw[mi+1][i]][i] > nlstate) {            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
           if (agedc[i] < 2*AGESUP) {  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          }
           if(j==0) j=1;  /* Survives at least one month after exam */          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
           k=k+1;  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
           if (j >= jmax) jmax=j;        }
           if (j <= jmin) jmin=j;        for(j=i+1; j<=nlstate+ndeath;j++){
           sum=sum+j;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
           }            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
         }  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
         else{          }
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
           k=k+1;        }
           if (j >= jmax) jmax=j;      }
           else if (j <= jmin)jmin=j;      
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      for(i=1; i<= nlstate; i++){
           sum=sum+j;        s1=0;
         }        for(j=1; j<i; j++){
         jk= j/stepm;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         jl= j -jk*stepm;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         ju= j -(jk+1)*stepm;        }
         if(jl <= -ju)        for(j=i+1; j<=nlstate+ndeath; j++){
           dh[mi][i]=jk;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         else          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           dh[mi][i]=jk+1;        }
         if(dh[mi][i]==0)        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
           dh[mi][i]=1; /* At least one step */        ps[i][i]=1./(s1+1.);
       }        /* Computing other pijs */
     }        for(j=1; j<i; j++)
   }          ps[i][j]= exp(ps[i][j])*ps[i][i];
   jmean=sum/k;        for(j=i+1; j<=nlstate+ndeath; j++)
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          ps[i][j]= exp(ps[i][j])*ps[i][i];
  }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 /*********** Tricode ****************************/      } /* end i */
 void tricode(int *Tvar, int **nbcode, int imx)      
 {      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   int Ndum[20],ij=1, k, j, i;        for(jj=1; jj<= nlstate+ndeath; jj++){
   int cptcode=0;          ps[ii][jj]=0;
   cptcoveff=0;          ps[ii][ii]=1;
          }
   for (k=0; k<19; k++) Ndum[k]=0;      }
   for (k=1; k<=7; k++) ncodemax[k]=0;      
       
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
     for (i=1; i<=imx; i++) {      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
       ij=(int)(covar[Tvar[j]][i]);      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       Ndum[ij]++;      /*   } */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      /*   printf("\n "); */
       if (ij > cptcode) cptcode=ij;      /* } */
     }      /* printf("\n ");printf("%lf ",cov[2]);*/
       /*
     for (i=0; i<=cptcode; i++) {        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       if(Ndum[i]!=0) ncodemax[j]++;        goto end;*/
     }      return ps;
     ij=1;  }
   
   /**************** Product of 2 matrices ******************/
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
         if (Ndum[k] != 0) {  {
           nbcode[Tvar[j]][ij]=k;    /* 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(...) */
           ij++;    /* in, b, out are matrice of pointers which should have been initialized 
         }       before: only the contents of out is modified. The function returns
         if (ij > ncodemax[j]) break;       a pointer to pointers identical to out */
       }      int i, j, k;
     }    for(i=nrl; i<= nrh; i++)
   }        for(k=ncolol; k<=ncoloh; k++){
         out[i][k]=0.;
  for (k=0; k<19; k++) Ndum[k]=0;        for(j=ncl; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
  for (i=1; i<=ncovmodel-2; i++) {      }
       ij=Tvar[i];    return out;
       Ndum[ij]++;  }
     }  
   
  ij=1;  /************* Higher Matrix Product ***************/
  for (i=1; i<=10; i++) {  
    if((Ndum[i]!=0) && (i<=ncovcol)){  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
      Tvaraff[ij]=i;  {
      ij++;    /* Computes the transition matrix starting at age 'age' over 
    }       'nhstepm*hstepm*stepm' months (i.e. until
  }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         nhstepm*hstepm matrices. 
     cptcoveff=ij-1;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 }       (typically every 2 years instead of every month which is too big 
        for the memory).
 /*********** Health Expectancies ****************/       Model is determined by parameters x and covariates have to be 
        included manually here. 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )  
        */
 {  
   /* Health expectancies */    int i, j, d, h, k;
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    double **out, cov[NCOVMAX+1];
   double age, agelim, hf;    double **newm;
   double ***p3mat,***varhe;  
   double **dnewm,**doldm;    /* Hstepm could be zero and should return the unit matrix */
   double *xp;    for (i=1;i<=nlstate+ndeath;i++)
   double **gp, **gm;      for (j=1;j<=nlstate+ndeath;j++){
   double ***gradg, ***trgradg;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   int theta;        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   xp=vector(1,npar);    for(h=1; h <=nhstepm; h++){
   dnewm=matrix(1,nlstate*2,1,npar);      for(d=1; d <=hstepm; d++){
   doldm=matrix(1,nlstate*2,1,nlstate*2);        newm=savm;
          /* Covariates have to be included here again */
   fprintf(ficreseij,"# Health expectancies\n");        cov[1]=1.;
   fprintf(ficreseij,"# Age");        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   for(i=1; i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) 
     for(j=1; j<=nlstate;j++)          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       fprintf(ficreseij," %1d-%1d (SE)",i,j);        for (k=1; k<=cptcovage;k++)
   fprintf(ficreseij,"\n");          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   if(estepm < stepm){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }  
   else  hstepm=estepm;          /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   /* We compute the life expectancy from trapezoids spaced every estepm months        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
    * This is mainly to measure the difference between two models: for example        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
    * if stepm=24 months pijx are given only every 2 years and by summing them                     pmij(pmmij,cov,ncovmodel,x,nlstate));
    * we are calculating an estimate of the Life Expectancy assuming a linear        savm=oldm;
    * progression inbetween and thus overestimating or underestimating according        oldm=newm;
    * 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      for(i=1; i<=nlstate+ndeath; i++)
    * to compare the new estimate of Life expectancy with the same linear        for(j=1;j<=nlstate+ndeath;j++) {
    * hypothesis. A more precise result, taking into account a more precise          po[i][j][h]=newm[i][j];
    * curvature will be obtained if estepm is as small as stepm. */          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         }
   /* For example we decided to compute the life expectancy with the smallest unit */      /*printf("h=%d ",h);*/
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    } /* end h */
      nhstepm is the number of hstepm from age to agelim  /*     printf("\n H=%d \n",h); */
      nstepm is the number of stepm from age to agelin.    return po;
      Look at hpijx to understand the reason of that which relies in memory size  }
      and note for a fixed period like estepm months */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  
      survival function given by stepm (the optimization length). Unfortunately it  /*************** log-likelihood *************/
      means that if the survival funtion is printed only each two years of age and if  double func( double *x)
      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.    int i, ii, j, k, mi, d, kk;
   */    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    double **out;
     double sw; /* Sum of weights */
   agelim=AGESUP;    double lli; /* Individual log likelihood */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int s1, s2;
     /* nhstepm age range expressed in number of stepm */    double bbh, survp;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    long ipmx;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    /*extern weight */
     /* if (stepm >= YEARM) hstepm=1;*/    /* We are differentiating ll according to initial status */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*for(i=1;i<imx;i++) 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);      printf(" %d\n",s[4][i]);
     gp=matrix(0,nhstepm,1,nlstate*2);    */
     gm=matrix(0,nhstepm,1,nlstate*2);    cov[1]=1.;
   
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    for(k=1; k<=nlstate; k++) ll[k]=0.;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      if(mle==1){
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         /* Computes the values of the ncovmodel covariates of the model
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
            Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
     /* Computing Variances of health expectancies */           to be observed in j being in i according to the model.
          */
      for(theta=1; theta <=npar; theta++){        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
       for(i=1; i<=npar; i++){          cov[2+k]=covar[Tvar[k]][i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        }
       }        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);             is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
             has been calculated etc */
       cptj=0;        for(mi=1; mi<= wav[i]-1; mi++){
       for(j=1; j<= nlstate; j++){          for (ii=1;ii<=nlstate+ndeath;ii++)
         for(i=1; i<=nlstate; i++){            for (j=1;j<=nlstate+ndeath;j++){
           cptj=cptj+1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;            }
           }          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                  for (kk=1; kk<=cptcovage;kk++) {
                    cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
       for(i=1; i<=npar; i++)            }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                  savm=oldm;
       cptj=0;            oldm=newm;
       for(j=1; j<= nlstate; j++){          } /* end mult */
         for(i=1;i<=nlstate;i++){        
           cptj=cptj+1;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){          /* But now since version 0.9 we anticipate for bias at large stepm.
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           }           * (in months) between two waves is not a multiple of stepm, we rounded to 
         }           * 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
                 * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
               * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       for(j=1; j<= nlstate*2; j++)           * -stepm/2 to stepm/2 .
         for(h=0; h<=nhstepm-1; h++){           * For stepm=1 the results are the same as for previous versions of Imach.
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];           * For stepm > 1 the results are less biased than in previous versions. 
         }           */
           s1=s[mw[mi][i]][i];
      }          s2=s[mw[mi+1][i]][i];
              bbh=(double)bh[mi][i]/(double)stepm; 
 /* End theta */          /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);           */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
      for(h=0; h<=nhstepm-1; h++)          if( s2 > nlstate){ 
       for(j=1; j<=nlstate*2;j++)            /* i.e. if s2 is a death state and if the date of death is known 
         for(theta=1; theta <=npar; theta++)               then the contribution to the likelihood is the probability to 
         trgradg[h][j][theta]=gradg[h][theta][j];               die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
                minus probability to die before dh-stepm . 
      for(i=1;i<=nlstate*2;i++)               In version up to 0.92 likelihood was computed
       for(j=1;j<=nlstate*2;j++)          as if date of death was unknown. Death was treated as any other
         varhe[i][j][(int)age] =0.;          health state: the date of the interview describes the actual state
           and not the date of a change in health state. The former idea was
      printf("%d|",(int)age);fflush(stdout);          to consider that at each interview the state was recorded
     for(h=0;h<=nhstepm-1;h++){          (healthy, disable or death) and IMaCh was corrected; but when we
       for(k=0;k<=nhstepm-1;k++){          introduced the exact date of death then we should have modified
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);          the contribution of an exact death to the likelihood. This new
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);          contribution is smaller and very dependent of the step unit
         for(i=1;i<=nlstate*2;i++)          stepm. It is no more the probability to die between last interview
           for(j=1;j<=nlstate*2;j++)          and month of death but the probability to survive from last
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          interview up to one month before death multiplied by the
       }          probability to die within a month. Thanks to Chris
     }          Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
                which slows down the processing. The difference can be up to 10%
     /* Computing expectancies */          lower mortality.
     for(i=1; i<=nlstate;i++)            */
       for(j=1; j<=nlstate;j++)            lli=log(out[s1][s2] - savm[s1][s2]);
         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;  
                    } else if  (s2==-2) {
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/            for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         }            /*survp += out[s1][j]; */
             lli= log(survp);
     fprintf(ficreseij,"%3.0f",age );          }
     cptj=0;          
     for(i=1; i<=nlstate;i++)          else if  (s2==-4) { 
       for(j=1; j<=nlstate;j++){            for (j=3,survp=0. ; j<=nlstate; j++)  
         cptj++;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );            lli= log(survp); 
       }          } 
     fprintf(ficreseij,"\n");  
              else if  (s2==-5) { 
     free_matrix(gm,0,nhstepm,1,nlstate*2);            for (j=1,survp=0. ; j<=2; j++)  
     free_matrix(gp,0,nhstepm,1,nlstate*2);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);            lli= log(survp); 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          } 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
   }          else{
   free_vector(xp,1,npar);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   free_matrix(dnewm,1,nlstate*2,1,npar);            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);          } 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 }          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
 /************ Variance ******************/          ipmx +=1;
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* Variance of health expectancies */        } /* end of wave */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      } /* end of individual */
   double **newm;    }  else if(mle==2){
   double **dnewm,**doldm;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i, j, nhstepm, hstepm, h, nstepm ;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int k, cptcode;        for(mi=1; mi<= wav[i]-1; mi++){
   double *xp;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double **gp, **gm;            for (j=1;j<=nlstate+ndeath;j++){
   double ***gradg, ***trgradg;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double ***p3mat;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double age,agelim, hf;            }
   int theta;          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficresvij,"# Age");            for (kk=1; kk<=cptcovage;kk++) {
   for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(j=1; j<=nlstate;j++)            }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   fprintf(ficresvij,"\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   xp=vector(1,npar);            oldm=newm;
   dnewm=matrix(1,nlstate,1,npar);          } /* end mult */
   doldm=matrix(1,nlstate,1,nlstate);        
            s1=s[mw[mi][i]][i];
   if(estepm < stepm){          s2=s[mw[mi+1][i]][i];
     printf ("Problem %d lower than %d\n",estepm, stepm);          bbh=(double)bh[mi][i]/(double)stepm; 
   }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   else  hstepm=estepm;            ipmx +=1;
   /* For example we decided to compute the life expectancy with the smallest unit */          sw += weight[i];
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      nhstepm is the number of hstepm from age to agelim        } /* end of wave */
      nstepm is the number of stepm from age to agelin.      } /* end of individual */
      Look at hpijx to understand the reason of that which relies in memory size    }  else if(mle==3){  /* exponential inter-extrapolation */
      and note for a fixed period like k years */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      survival function given by stepm (the optimization length). Unfortunately it        for(mi=1; mi<= wav[i]-1; mi++){
      means that if the survival funtion is printed only each two years of age and if          for (ii=1;ii<=nlstate+ndeath;ii++)
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            for (j=1;j<=nlstate+ndeath;j++){
      results. So we changed our mind and took the option of the best precision.              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            }
   agelim = AGESUP;          for(d=0; d<dh[mi][i]; d++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            newm=savm;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            for (kk=1; kk<=cptcovage;kk++) {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);            }
     gp=matrix(0,nhstepm,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     gm=matrix(0,nhstepm,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     for(theta=1; theta <=npar; theta++){            oldm=newm;
       for(i=1; i<=npar; i++){ /* Computes gradient */          } /* end mult */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        
       }          s1=s[mw[mi][i]][i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            s2=s[mw[mi+1][i]][i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       if (popbased==1) {          ipmx +=1;
         for(i=1; i<=nlstate;i++)          sw += weight[i];
           prlim[i][i]=probs[(int)age][i][ij];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }        } /* end of wave */
        } /* end of individual */
       for(j=1; j<= nlstate; j++){    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         for(h=0; h<=nhstepm; h++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        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);
       for(i=1; i<=npar; i++) /* Computes gradient */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for(d=0; d<dh[mi][i]; d++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if (popbased==1) {            for (kk=1; kk<=cptcovage;kk++) {
         for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           prlim[i][i]=probs[(int)age][i][ij];            }
       }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(j=1; j<= nlstate; j++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(h=0; h<=nhstepm; h++){            savm=oldm;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            oldm=newm;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          } /* end mult */
         }        
       }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
       for(j=1; j<= nlstate; j++)          if( s2 > nlstate){ 
         for(h=0; h<=nhstepm; h++){            lli=log(out[s1][s2] - savm[s1][s2]);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          }else{
         }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     } /* End theta */          }
           ipmx +=1;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(h=0; h<=nhstepm; h++)  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       for(j=1; j<=nlstate;j++)        } /* end of wave */
         for(theta=1; theta <=npar; theta++)      } /* end of individual */
           trgradg[h][j][theta]=gradg[h][theta][j];    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        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++){
       for(j=1;j<=nlstate;j++)          for (ii=1;ii<=nlstate+ndeath;ii++)
         vareij[i][j][(int)age] =0.;            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(h=0;h<=nhstepm;h++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(k=0;k<=nhstepm;k++){            }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          for(d=0; d<dh[mi][i]; d++){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            newm=savm;
         for(i=1;i<=nlstate;i++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(j=1;j<=nlstate;j++)            for (kk=1; kk<=cptcovage;kk++) {
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
     }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     fprintf(ficresvij,"%.0f ",age );                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i=1; i<=nlstate;i++)            savm=oldm;
       for(j=1; j<=nlstate;j++){            oldm=newm;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          } /* end mult */
       }        
     fprintf(ficresvij,"\n");          s1=s[mw[mi][i]][i];
     free_matrix(gp,0,nhstepm,1,nlstate);          s2=s[mw[mi+1][i]][i];
     free_matrix(gm,0,nhstepm,1,nlstate);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          ipmx +=1;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          sw += weight[i];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   } /* End age */          /*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 */
   free_vector(xp,1,npar);      } /* end of individual */
   free_matrix(doldm,1,nlstate,1,npar);    } /* End of if */
   free_matrix(dnewm,1,nlstate,1,nlstate);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     return -l;
 /************ 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)  
 {  /*************** log-likelihood *************/
   /* Variance of prevalence limit */  double funcone( double *x)
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  {
   double **newm;    /* Same as likeli but slower because of a lot of printf and if */
   double **dnewm,**doldm;    int i, ii, j, k, mi, d, kk;
   int i, j, nhstepm, hstepm;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   int k, cptcode;    double **out;
   double *xp;    double lli; /* Individual log likelihood */
   double *gp, *gm;    double llt;
   double **gradg, **trgradg;    int s1, s2;
   double age,agelim;    double bbh, survp;
   int theta;    /*extern weight */
        /* We are differentiating ll according to initial status */
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   fprintf(ficresvpl,"# Age");    /*for(i=1;i<imx;i++) 
   for(i=1; i<=nlstate;i++)      printf(" %d\n",s[4][i]);
       fprintf(ficresvpl," %1d-%1d",i,i);    */
   fprintf(ficresvpl,"\n");    cov[1]=1.;
   
   xp=vector(1,npar);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   hstepm=1*YEARM; /* Every year of age */      for(mi=1; mi<= wav[i]-1; mi++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        for (ii=1;ii<=nlstate+ndeath;ii++)
   agelim = AGESUP;          for (j=1;j<=nlstate+ndeath;j++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (stepm >= YEARM) hstepm=1;          }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        for(d=0; d<dh[mi][i]; d++){
     gradg=matrix(1,npar,1,nlstate);          newm=savm;
     gp=vector(1,nlstate);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     gm=vector(1,nlstate);          for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(theta=1; theta <=npar; theta++){          }
       for(i=1; i<=npar; i++){ /* Computes gradient */          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
       for(i=1;i<=nlstate;i++)          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
         gp[i] = prlim[i][i];          savm=oldm;
              oldm=newm;
       for(i=1; i<=npar; i++) /* Computes gradient */        } /* end mult */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        s1=s[mw[mi][i]][i];
       for(i=1;i<=nlstate;i++)        s2=s[mw[mi+1][i]][i];
         gm[i] = prlim[i][i];        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
       for(i=1;i<=nlstate;i++)         * is higher than the multiple of stepm and negative otherwise.
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];         */
     } /* End theta */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
     trgradg =matrix(1,nlstate,1,npar);        } else if  (s2==-2) {
           for (j=1,survp=0. ; j<=nlstate; j++) 
     for(j=1; j<=nlstate;j++)            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       for(theta=1; theta <=npar; theta++)          lli= log(survp);
         trgradg[j][theta]=gradg[theta][j];        }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     for(i=1;i<=nlstate;i++)        } else if(mle==2){
       varpl[i][(int)age] =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 */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        } else if(mle==3){  /* exponential inter-extrapolation */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     for(i=1;i<=nlstate;i++)        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          lli=log(out[s1][s2]); /* Original formula */
         } else{  /* mle=0 back to 1 */
     fprintf(ficresvpl,"%.0f ",age );          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     for(i=1; i<=nlstate;i++)          /*lli=log(out[s1][s2]); */ /* Original formula */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        } /* End of if */
     fprintf(ficresvpl,"\n");        ipmx +=1;
     free_vector(gp,1,nlstate);        sw += weight[i];
     free_vector(gm,1,nlstate);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     free_matrix(gradg,1,npar,1,nlstate);        /*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]); */
     free_matrix(trgradg,1,nlstate,1,npar);        if(globpr){
   } /* End age */          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
    %11.6f %11.6f %11.6f ", \
   free_vector(xp,1,npar);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   free_matrix(doldm,1,nlstate,1,npar);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   free_matrix(dnewm,1,nlstate,1,nlstate);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
 }            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
 /************ Variance of one-step probabilities  ******************/          fprintf(ficresilk," %10.6f\n", -llt);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)        }
 {      } /* end of wave */
   int i, j, i1, k1, j1, z1;    } /* end of individual */
   int k=0, cptcode;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   double **dnewm,**doldm;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   double *xp;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   double *gp, *gm;    if(globpr==0){ /* First time we count the contributions and weights */
   double **gradg, **trgradg;      gipmx=ipmx;
   double age,agelim, cov[NCOVMAX];      gsw=sw;
   int theta;    }
   char fileresprob[FILENAMELENGTH];    return -l;
   }
   strcpy(fileresprob,"prob");  
   strcat(fileresprob,fileres);  
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  /*************** function likelione ***********/
     printf("Problem with resultfile: %s\n", fileresprob);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   }  {
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    /* This routine should help understanding what is done with 
         the selection of individuals/waves and
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");       to check the exact contribution to the likelihood.
   fprintf(ficresprob,"# Age");       Plotting could be done.
   for(i=1; i<=nlstate;i++)     */
     for(j=1; j<=(nlstate+ndeath);j++)    int k;
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  
     if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
   fprintf(ficresprob,"\n");      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
   xp=vector(1,npar);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      }
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
        fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   cov[1]=1;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   j=cptcoveff;      for(k=1; k<=nlstate; k++) 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   j1=0;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   for(k1=1; k1<=1;k1++){    }
     for(i1=1; i1<=ncodemax[k1];i1++){  
     j1++;    *fretone=(*funcone)(p);
     if(*globpri !=0){
     if  (cptcovn>0) {      fclose(ficresilk);
       fprintf(ficresprob, "\n#********** Variable ");      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      fflush(fichtm); 
       fprintf(ficresprob, "**********\n#");    } 
     }    return;
      }
       for (age=bage; age<=fage; age ++){  
         cov[2]=age;  
         for (k=1; k<=cptcovn;k++) {  /*********** Maximum Likelihood Estimation ***************/
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];  
            void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         }  {
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    int i,j, iter;
         for (k=1; k<=cptcovprod;k++)    double **xi;
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    double fret;
            double fretone; /* Only one call to likelihood */
         gradg=matrix(1,npar,1,9);    /*  char filerespow[FILENAMELENGTH];*/
         trgradg=matrix(1,9,1,npar);    xi=matrix(1,npar,1,npar);
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    for (i=1;i<=npar;i++)
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      for (j=1;j<=npar;j++)
            xi[i][j]=(i==j ? 1.0 : 0.0);
         for(theta=1; theta <=npar; theta++){    printf("Powell\n");  fprintf(ficlog,"Powell\n");
           for(i=1; i<=npar; i++)    strcpy(filerespow,"pow"); 
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    strcat(filerespow,fileres);
              if((ficrespow=fopen(filerespow,"w"))==NULL) {
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      printf("Problem with resultfile: %s\n", filerespow);
                fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
           k=0;    }
           for(i=1; i<= (nlstate+ndeath); i++){    fprintf(ficrespow,"# Powell\n# iter -2*LL");
             for(j=1; j<=(nlstate+ndeath);j++){    for (i=1;i<=nlstate;i++)
               k=k+1;      for(j=1;j<=nlstate+ndeath;j++)
               gp[k]=pmmij[i][j];        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
             }    fprintf(ficrespow,"\n");
           }  
              powell(p,xi,npar,ftol,&iter,&fret,func);
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    free_matrix(xi,1,npar,1,npar);
        fclose(ficrespow);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
           k=0;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           for(i=1; i<=(nlstate+ndeath); i++){    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;  }
               gm[k]=pmmij[i][j];  
             }  /**** Computes Hessian and covariance matrix ***/
           }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
        {
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    double  **a,**y,*x,pd;
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      double **hess;
         }    int i, j,jk;
     int *indx;
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  
           for(theta=1; theta <=npar; theta++)    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
             trgradg[j][theta]=gradg[theta][j];    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
            void lubksb(double **a, int npar, int *indx, double b[]) ;
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    void ludcmp(double **a, int npar, int *indx, double *d) ;
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    double gompertz(double p[]);
            hess=matrix(1,npar,1,npar);
         pmij(pmmij,cov,ncovmodel,x,nlstate);  
            printf("\nCalculation of the hessian matrix. Wait...\n");
         k=0;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         for(i=1; i<=(nlstate+ndeath); i++){    for (i=1;i<=npar;i++){
           for(j=1; j<=(nlstate+ndeath);j++){      printf("%d",i);fflush(stdout);
             k=k+1;      fprintf(ficlog,"%d",i);fflush(ficlog);
             gm[k]=pmmij[i][j];     
           }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
         }      
            /*  printf(" %f ",p[i]);
      /*printf("\n%d ",(int)age);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    
      }*/    for (i=1;i<=npar;i++) {
       for (j=1;j<=npar;j++)  {
         fprintf(ficresprob,"\n%d ",(int)age);        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));          hess[i][j]=hessij(p,delti,i,j,func,npar);
            
       }          hess[j][i]=hess[i][j];    
     }          /*printf(" %lf ",hess[i][j]);*/
     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);    printf("\n");
   }    fprintf(ficlog,"\n");
   free_vector(xp,1,npar);  
   fclose(ficresprob);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
      fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 }    
     a=matrix(1,npar,1,npar);
 /******************* Printing html file ***********/    y=matrix(1,npar,1,npar);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    x=vector(1,npar);
                   int lastpass, int stepm, int weightopt, char model[],\    indx=ivector(1,npar);
                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    for (i=1;i<=npar;i++)
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
                   char version[], int popforecast, int estepm ,/* \ */    ludcmp(a,npar,indx,&pd);
                   double jprev1, double mprev1,double anprev1, \  
                   double jprev2, double mprev2,double anprev2){    for (j=1;j<=npar;j++) {
   int jj1, k1, i1, cpt;      for (i=1;i<=npar;i++) x[i]=0;
   FILE *fichtm;      x[j]=1;
   /*char optionfilehtm[FILENAMELENGTH];*/      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   strcpy(optionfilehtm,optionfile);        matcov[i][j]=x[i];
   strcat(optionfilehtm,".htm");      }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    }
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }    printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    for (i=1;i<=npar;i++) { 
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n      for (j=1;j<=npar;j++) { 
 \n        printf("%.3e ",hess[i][j]);
 Total number of observations=%d <br>\n        fprintf(ficlog,"%.3e ",hess[i][j]);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      }
 <hr  size=\"2\" color=\"#EC5E5E\">      printf("\n");
  <ul><li>Parameter files<br>\n      fprintf(ficlog,"\n");
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    }
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);  
     /* Recompute Inverse */
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n    for (i=1;i<=npar;i++)
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    ludcmp(a,npar,indx,&pd);
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n  
  - Life expectancies by age and initial health status (estepm=%2d months):    /*  printf("\n#Hessian matrix recomputed#\n");
    <a href=\"e%s\">e%s</a> <br>\n</li>", \  
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n      x[j]=1;
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n      lubksb(a,npar,indx,x);
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      for (i=1;i<=npar;i++){ 
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n        y[i][j]=x[i];
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n        printf("%.3e ",y[i][j]);
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);        fprintf(ficlog,"%.3e ",y[i][j]);
       }
  if(popforecast==1) fprintf(fichtm,"\n      printf("\n");
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      fprintf(ficlog,"\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);    free_matrix(a,1,npar,1,npar);
 fprintf(fichtm," <li>Graphs</li><p>");    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
  m=cptcoveff;    free_ivector(indx,1,npar);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    free_matrix(hess,1,npar,1,npar);
   
  jj1=0;  
  for(k1=1; k1<=m;k1++){  }
    for(i1=1; i1<=ncodemax[k1];i1++){  
        jj1++;  /*************** hessian matrix ****************/
        if (cptcovn > 0) {  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  {
          for (cpt=1; cpt<=cptcoveff;cpt++)    int i;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    int l=1, lmax=20;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    double k1,k2;
        }    double p2[MAXPARM+1]; /* identical to x */
        /* Pij */    double res;
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
 <img src=\"pe%s%d1.png\">",strtok(optionfile, "."),jj1,stepm,strtok(optionfile, "."),jj1);        double fx;
        /* Quasi-incidences */    int k=0,kmax=10;
        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: pe%s%d2.png<br>    double l1;
 <img src=\"pe%s%d2.png\">",strtok(optionfile, "."),jj1,stepm,strtok(optionfile, "."),jj1);      
        /* Stable prevalence in each health state */    fx=func(x);
        for(cpt=1; cpt<nlstate;cpt++){    for (i=1;i<=npar;i++) p2[i]=x[i];
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      l1=pow(10,l);
        }      delts=delt;
     for(cpt=1; cpt<=nlstate;cpt++) {      for(k=1 ; k <kmax; k=k+1){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        delt = delta*(l1*k);
 interval) in state (%d): v%s%d%d.png <br>        p2[theta]=x[theta] +delt;
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
      }        p2[theta]=x[theta]-delt;
      for(cpt=1; cpt<=nlstate;cpt++) {        k2=func(p2)-fx;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>        /*res= (k1-2.0*fx+k2)/delt/delt; */
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
      }        
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  #ifdef DEBUGHESS
 health expectancies in states (1) and (2): e%s%d.png<br>        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);
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        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);
 fprintf(fichtm,"\n</body>");  #endif
    }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
    }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
 fclose(fichtm);          k=kmax;
 }        }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 /******************* Gnuplot file **************/          k=kmax; l=lmax*10.;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          delts=delt;
   int ng;        }
   strcpy(optionfilegnuplot,optionfilefiname);      }
   strcat(optionfilegnuplot,".gp.txt");    }
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    delti[theta]=delts;
     printf("Problem with file %s",optionfilegnuplot);    return res; 
   }    
   }
 #ifdef windows  
     fprintf(ficgp,"cd \"%s\" \n",pathc);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 #endif  {
 m=pow(2,cptcoveff);    int i;
      int l=1, l1, lmax=20;
  /* 1eme*/    double k1,k2,k3,k4,res,fx;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    double p2[MAXPARM+1];
    for (k1=1; k1<= m ; k1 ++) {    int k;
   
 #ifdef windows    fx=func(x);
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    for (k=1; k<=2; k++) {
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);      for (i=1;i<=npar;i++) p2[i]=x[i];
 #endif      p2[thetai]=x[thetai]+delti[thetai]/k;
 #ifdef unix      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      k1=func(p2)-fx;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    
 #endif      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 for (i=1; i<= nlstate ; i ++) {      k2=func(p2)-fx;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");      p2[thetai]=x[thetai]-delti[thetai]/k;
 }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      k3=func(p2)-fx;
     for (i=1; i<= nlstate ; i ++) {    
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      p2[thetai]=x[thetai]-delti[thetai]/k;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 }      k4=func(p2)-fx;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
      for (i=1; i<= nlstate ; i ++) {  #ifdef DEBUG
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
 }    #endif
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    }
 #ifdef unix    return res;
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");  }
 #endif  
    }  /************** Inverse of matrix **************/
   }  void ludcmp(double **a, int n, int *indx, double *d) 
   /*2 eme*/  { 
     int i,imax,j,k; 
   for (k1=1; k1<= m ; k1 ++) {    double big,dum,sum,temp; 
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);    double *vv; 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);   
        vv=vector(1,n); 
     for (i=1; i<= nlstate+1 ; i ++) {    *d=1.0; 
       k=2*i;    for (i=1;i<=n;i++) { 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      big=0.0; 
       for (j=1; j<= nlstate+1 ; j ++) {      for (j=1;j<=n;j++) 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if ((temp=fabs(a[i][j])) > big) big=temp; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 }        vv[i]=1.0/big; 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    } 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    for (j=1;j<=n;j++) { 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      for (i=1;i<j;i++) { 
       for (j=1; j<= nlstate+1 ; j ++) {        sum=a[i][j]; 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         else fprintf(ficgp," \%%*lf (\%%*lf)");        a[i][j]=sum; 
 }        } 
       fprintf(ficgp,"\" t\"\" w l 0,");      big=0.0; 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      for (i=j;i<=n;i++) { 
       for (j=1; j<= nlstate+1 ; j ++) {        sum=a[i][j]; 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for (k=1;k<j;k++) 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          sum -= a[i][k]*a[k][j]; 
 }          a[i][j]=sum; 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       else fprintf(ficgp,"\" t\"\" w l 0,");          big=dum; 
     }          imax=i; 
   }        } 
        } 
   /*3eme*/      if (j != imax) { 
         for (k=1;k<=n;k++) { 
   for (k1=1; k1<= m ; k1 ++) {          dum=a[imax][k]; 
     for (cpt=1; cpt<= nlstate ; cpt ++) {          a[imax][k]=a[j][k]; 
       k=2+nlstate*(2*cpt-2);          a[j][k]=dum; 
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        } 
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        *d = -(*d); 
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        vv[imax]=vv[j]; 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      } 
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      indx[j]=imax; 
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      if (a[j][j] == 0.0) a[j][j]=TINY; 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      if (j != n) { 
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
 */      } 
       for (i=1; i< nlstate ; i ++) {    } 
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);    free_vector(vv,1,n);  /* Doesn't work */
   ;
       }  } 
     }  
   }  void lubksb(double **a, int n, int *indx, double b[]) 
    { 
   /* CV preval stat */    int i,ii=0,ip,j; 
     for (k1=1; k1<= m ; k1 ++) {    double sum; 
     for (cpt=1; cpt<nlstate ; cpt ++) {   
       k=3;    for (i=1;i<=n;i++) { 
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      ip=indx[i]; 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);      sum=b[ip]; 
       b[ip]=b[i]; 
       for (i=1; i< nlstate ; i ++)      if (ii) 
         fprintf(ficgp,"+$%d",k+i+1);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      else if (sum) ii=i; 
            b[i]=sum; 
       l=3+(nlstate+ndeath)*cpt;    } 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    for (i=n;i>=1;i--) { 
       for (i=1; i< nlstate ; i ++) {      sum=b[i]; 
         l=3+(nlstate+ndeath)*cpt;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         fprintf(ficgp,"+$%d",l+i+1);      b[i]=sum/a[i][i]; 
       }    } 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    } 
     }  
   }    void pstamp(FILE *fichier)
    {
   /* proba elementaires */    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
    for(i=1,jk=1; i <=nlstate; i++){  }
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {  /************ Frequencies ********************/
         for(j=1; j <=ncovmodel; j++){  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
          {  /* Some frequencies */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    
           jk++;    int i, m, jk, k1,i1, j1, bool, z1,j;
           fprintf(ficgp,"\n");    int first;
         }    double ***freq; /* Frequencies */
       }    double *pp, **prop;
     }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
    }    char fileresp[FILENAMELENGTH];
     
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    pp=vector(1,nlstate);
      for(jk=1; jk <=m; jk++) {    prop=matrix(1,nlstate,iagemin,iagemax+3);
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    strcpy(fileresp,"p");
        if (ng==2)    strcat(fileresp,fileres);
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    if((ficresp=fopen(fileresp,"w"))==NULL) {
        else      printf("Problem with prevalence resultfile: %s\n", fileresp);
          fprintf(ficgp,"\nset title \"Probability\"\n");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);      exit(0);
        i=1;    }
        for(k2=1; k2<=nlstate; k2++) {    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
          k3=i;    j1=0;
          for(k=1; k<=(nlstate+ndeath); k++) {    
            if (k != k2){    j=cptcoveff;
              if(ng==2)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
                fprintf(ficgp," %f*exp(p%d+p%d*x",stepm/YEARM,i,i+1);  
              else    first=1;
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  
              ij=1;    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
              for(j=3; j <=ncovmodel; j++) {    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /*    j1++;
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  */
                  ij++;    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
                }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                else          scanf("%d", i);*/
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        for (i=-5; i<=nlstate+ndeath; i++)  
              }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
              fprintf(ficgp,")/(1");            for(m=iagemin; m <= iagemax+3; m++)
                            freq[i][jk][m]=0;
              for(k1=1; k1 <=nlstate; k1++){          
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        for (i=1; i<=nlstate; i++)  
                ij=1;          for(m=iagemin; m <= iagemax+3; m++)
                for(j=3; j <=ncovmodel; j++){            prop[i][m]=0;
                  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]]]);        dateintsum=0;
                    ij++;        k2cpt=0;
                  }        for (i=1; i<=imx; i++) {
                  else          bool=1;
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                }            for (z1=1; z1<=cptcoveff; z1++)       
                fprintf(ficgp,")");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
              }                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);                bool=0;
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                /* 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", 
              i=i+ncovmodel;                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
            }                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
          }                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
        }              } 
      }          }
    }   
    fclose(ficgp);          if (bool==1){
 }  /* end gnuplot */            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 /*************** Moving average **************/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){                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];
   int i, cpt, cptcod;                if (m<lastpass) {
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       for (i=1; i<=nlstate;i++)                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)                }
           mobaverage[(int)agedeb][i][cptcod]=0.;                
                    if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){                  dateintsum=dateintsum+k2;
       for (i=1; i<=nlstate;i++){                  k2cpt++;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                }
           for (cpt=0;cpt<=4;cpt++){                /*}*/
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];            }
           }          }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        } /* end i */
         }         
       }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     }        pstamp(ficresp);
            if  (cptcovn>0) {
 }          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
 /************** Forecasting ******************/          fprintf(ficlog, "\n#********** Variable "); 
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficlog, "**********\n#");
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        }
   int *popage;        for(i=1; i<=nlstate;i++) 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   double *popeffectif,*popcount;        fprintf(ficresp, "\n");
   double ***p3mat;        
   char fileresf[FILENAMELENGTH];        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
  agelim=AGESUP;            fprintf(ficlog,"Total");
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          }else{
             if(first==1){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              first=0;
                printf("See log file for details...\n");
              }
   strcpy(fileresf,"f");            fprintf(ficlog,"Age %d", i);
   strcat(fileresf,fileres);          }
   if((ficresf=fopen(fileresf,"w"))==NULL) {          for(jk=1; jk <=nlstate ; jk++){
     printf("Problem with forecast resultfile: %s\n", fileresf);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   }              pp[jk] += freq[jk][m][i]; 
   printf("Computing forecasting: result on file '%s' \n", fileresf);          }
           for(jk=1; jk <=nlstate ; jk++){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
   if (mobilav==1) {            if(pp[jk]>=1.e-10){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              if(first==1){
     movingaverage(agedeb, fage, ageminpar, mobaverage);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }              }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   stepsize=(int) (stepm+YEARM-1)/YEARM;            }else{
   if (stepm<=12) stepsize=1;              if(first==1)
                  printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   agelim=AGESUP;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
              }
   hstepm=1;          }
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);          for(jk=1; jk <=nlstate ; jk++){
   anprojmean=yp;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   yp2=modf((yp1*12),&yp);              pp[jk] += freq[jk][m][i];
   mprojmean=yp;          }       
   yp1=modf((yp2*30.5),&yp);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   jprojmean=yp;            pos += pp[jk];
   if(jprojmean==0) jprojmean=1;            posprop += prop[jk][i];
   if(mprojmean==0) jprojmean=1;          }
            for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);            if(pos>=1.e-5){
                if(first==1)
   for(cptcov=1;cptcov<=i2;cptcov++){                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       k=k+1;            }else{
       fprintf(ficresf,"\n#******");              if(first==1)
       for(j=1;j<=cptcoveff;j++) {                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       }            }
       fprintf(ficresf,"******\n");            if( i <= iagemax){
       fprintf(ficresf,"# StartingAge FinalAge");              if(pos>=1.e-5){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                      /*probs[i][jk][j1]= pp[jk]/pos;*/
                      /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {              }
         fprintf(ficresf,"\n");              else
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                  fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          
           nhstepm = nhstepm/hstepm;          for(jk=-1; jk <=nlstate+ndeath; jk++)
                      for(m=-1; m <=nlstate+ndeath; m++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              if(freq[jk][m][i] !=0 ) {
           oldm=oldms;savm=savms;              if(first==1)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                        fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
           for (h=0; h<=nhstepm; h++){              }
             if (h==(int) (calagedate+YEARM*cpt)) {          if(i <= iagemax)
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);            fprintf(ficresp,"\n");
             }          if(first==1)
             for(j=1; j<=nlstate+ndeath;j++) {            printf("Others in log...\n");
               kk1=0.;kk2=0;          fprintf(ficlog,"\n");
               for(i=1; i<=nlstate;i++) {                      }
                 if (mobilav==1)        /*}*/
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    }
                 else {    dateintmean=dateintsum/k2cpt; 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];   
                 }    fclose(ficresp);
                    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
               }    free_vector(pp,1,nlstate);
               if (h==(int)(calagedate+12*cpt)){    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
                 fprintf(ficresf," %.3f", kk1);    /* End of Freq */
                          }
               }  
             }  /************ Prevalence ********************/
           }  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {  
         }    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       }       in each health status at the date of interview (if between dateprev1 and dateprev2).
     }       We still use firstpass and lastpass as another selection.
   }    */
           
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int i, m, jk, k1, i1, j1, bool, z1,j;
     double ***freq; /* Frequencies */
   fclose(ficresf);    double *pp, **prop;
 }    double pos,posprop; 
 /************** Forecasting ******************/    double  y2; /* in fractional years */
 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 iagemin, iagemax;
      int first; /** to stop verbosity which is redirected to log file */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;    iagemin= (int) agemin;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    iagemax= (int) agemax;
   double *popeffectif,*popcount;    /*pp=vector(1,nlstate);*/
   double ***p3mat,***tabpop,***tabpopprev;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   char filerespop[FILENAMELENGTH];    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*j=cptcoveff;*/
   agelim=AGESUP;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    
      first=1;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
        /*for(i1=1; i1<=ncodemax[k1];i1++){
          j1++;*/
   strcpy(filerespop,"pop");        
   strcat(filerespop,fileres);        for (i=1; i<=nlstate; i++)  
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          for(m=iagemin; m <= iagemax+3; m++)
     printf("Problem with forecast resultfile: %s\n", filerespop);            prop[i][m]=0.0;
   }       
   printf("Computing forecasting: result on file '%s' \n", filerespop);        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   if (mobilav==1) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                bool=0;
     movingaverage(agedeb, fage, ageminpar, mobaverage);          } 
   }          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   if (stepm<=12) stepsize=1;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                  if(agev[m][i]==0) agev[m][i]=iagemax+1;
   agelim=AGESUP;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                  if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   hstepm=1;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   hstepm=hstepm/stepm;                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                    prop[s[m][i]][(int)agev[m][i]] += weight[i];
   if (popforecast==1) {                  prop[s[m][i]][iagemax+3] += weight[i]; 
     if((ficpop=fopen(popfile,"r"))==NULL) {                } 
       printf("Problem with population file : %s\n",popfile);exit(0);              }
     }            } /* end selection of waves */
     popage=ivector(0,AGESUP);          }
     popeffectif=vector(0,AGESUP);        }
     popcount=vector(0,AGESUP);        for(i=iagemin; i <= iagemax+3; i++){  
              for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     i=1;              posprop += prop[jk][i]; 
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          } 
              
     imx=i;          for(jk=1; jk <=nlstate ; jk++){     
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            if( i <=  iagemax){ 
   }              if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
   for(cptcov=1;cptcov<=i2;cptcov++){              } else{
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                if(first==1){
       k=k+1;                  first=0;
       fprintf(ficrespop,"\n#******");                  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]);
       for(j=1;j<=cptcoveff;j++) {                }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              }
       }            } 
       fprintf(ficrespop,"******\n");          }/* end jk */ 
       fprintf(ficrespop,"# Age");        }/* end i */ 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      /*} *//* end i1 */
       if (popforecast==1)  fprintf(ficrespop," [Population]");    } /* end j1 */
          
       for (cpt=0; cpt<=0;cpt++) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      /*free_vector(pp,1,nlstate);*/
            free_matrix(prop,1,nlstate, iagemin,iagemax+3);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  }  /* End of prevalence */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;  /************* Waves Concatenation ***************/
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  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)
           oldm=oldms;savm=savms;  {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
               Death is a valid wave (if date is known).
           for (h=0; h<=nhstepm; h++){       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
             if (h==(int) (calagedate+YEARM*cpt)) {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);       and mw[mi+1][i]. dh depends on stepm.
             }       */
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;    int i, mi, m;
               for(i=1; i<=nlstate;i++) {                  /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
                 if (mobilav==1)       double sum=0., jmean=0.;*/
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    int first;
                 else {    int j, k=0,jk, ju, jl;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    double sum=0.;
                 }    first=0;
               }    jmin=1e+5;
               if (h==(int)(calagedate+12*cpt)){    jmax=-1;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    jmean=0.;
                   /*fprintf(ficrespop," %.3f", kk1);    for(i=1; i<=imx; i++){
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/      mi=0;
               }      m=firstpass;
             }      while(s[m][i] <= nlstate){
             for(i=1; i<=nlstate;i++){        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
               kk1=0.;          mw[++mi][i]=m;
                 for(j=1; j<=nlstate;j++){        if(m >=lastpass)
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          break;
                 }        else
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];          m++;
             }      }/* end while */
       if (s[m][i] > nlstate){
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        mi++;     /* Death is another wave */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        /* if(mi==0)  never been interviewed correctly before death */
           }           /* Only death is a correct wave */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        mw[mi][i]=m;
         }      }
       }  
        wav[i]=mi;
   /******/      if(mi==0){
         nbwarn++;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        if(first==0){
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          first=1;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        }
           nhstepm = nhstepm/hstepm;        if(first==1){
                    fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
           oldm=oldms;savm=savms;      } /* end mi==0 */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      } /* End individuals */
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    for(i=1; i<=imx; i++){
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      for(mi=1; mi<wav[i];mi++){
             }        if (stepm <=0)
             for(j=1; j<=nlstate+ndeath;j++) {          dh[mi][i]=1;
               kk1=0.;kk2=0;        else{
               for(i=1; i<=nlstate;i++) {                        if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                if (agedc[i] < 2*AGESUP) {
               }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);              if(j==0) j=1;  /* Survives at least one month after exam */
             }              else if(j<0){
           }                nberr++;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         }                j=1; /* Temporary Dangerous patch */
       }                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
    }                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              k=k+1;
               if (j >= jmax){
   if (popforecast==1) {                jmax=j;
     free_ivector(popage,0,AGESUP);                ijmax=i;
     free_vector(popeffectif,0,AGESUP);              }
     free_vector(popcount,0,AGESUP);              if (j <= jmin){
   }                jmin=j;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                ijmin=i;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              }
   fclose(ficrespop);              sum=sum+j;
 }              /*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);*/
 /***********************************************/            }
 /**************** Main Program *****************/          }
 /***********************************************/          else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 int main(int argc, char *argv[])  /*        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]); */
 {  
             k=k+1;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;            if (j >= jmax) {
   double agedeb, agefin,hf;              jmax=j;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;              ijmax=i;
             }
   double fret;            else if (j <= jmin){
   double **xi,tmp,delta;              jmin=j;
               ijmin=i;
   double dum; /* Dummy variable */            }
   double ***p3mat;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   int *indx;            /*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]);*/
   char line[MAXLINE], linepar[MAXLINE];            if(j<0){
   char title[MAXLINE];              nberr++;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];              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]);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];              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]);
              }
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];            sum=sum+j;
           }
   char filerest[FILENAMELENGTH];          jk= j/stepm;
   char fileregp[FILENAMELENGTH];          jl= j -jk*stepm;
   char popfile[FILENAMELENGTH];          ju= j -(jk+1)*stepm;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   int firstobs=1, lastobs=10;            if(jl==0){
   int sdeb, sfin; /* Status at beginning and end */              dh[mi][i]=jk;
   int c,  h , cpt,l;              bh[mi][i]=0;
   int ju,jl, mi;            }else{ /* We want a negative bias in order to only have interpolation ie
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;                    * to avoid the price of an extra matrix product in likelihood */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;              dh[mi][i]=jk+1;
   int mobilav=0,popforecast=0;              bh[mi][i]=ju;
   int hstepm, nhstepm;            }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;          }else{
             if(jl <= -ju){
   double bage, fage, age, agelim, agebase;              dh[mi][i]=jk;
   double ftolpl=FTOL;              bh[mi][i]=jl;       /* bias is positive if real duration
   double **prlim;                                   * is higher than the multiple of stepm and negative otherwise.
   double *severity;                                   */
   double ***param; /* Matrix of parameters */            }
   double  *p;            else{
   double **matcov; /* Matrix of covariance */              dh[mi][i]=jk+1;
   double ***delti3; /* Scale */              bh[mi][i]=ju;
   double *delti; /* Scale */            }
   double ***eij, ***vareij;            if(dh[mi][i]==0){
   double **varpl; /* Variances of prevalence limits by age */              dh[mi][i]=1; /* At least one step */
   double *epj, vepp;              bh[mi][i]=ju; /* At least one step */
   double kk1, kk2;              /*  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);*/
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;            }
            } /* end if mle */
         }
   char version[80]="Imach version 0.8e, May 2002, INED-EUROREVES ";      } /* end wave */
   char *alph[]={"a","a","b","c","d","e"}, str[4];    }
     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);
   char z[1]="c", occ;    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);
 #include <sys/time.h>   }
 #include <time.h>  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  /*********** Tricode ****************************/
    void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   /* long total_usecs;  {
   struct timeval start_time, end_time;    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
      /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
   getcwd(pathcd, size);     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
     /* nbcode[Tvar[j]][1]= 
   printf("\n%s",version);    */
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     scanf("%s",pathtot);    int modmaxcovj=0; /* Modality max of covariates j */
   }    int cptcode=0; /* Modality max of covariates j */
   else{    int modmincovj=0; /* Modality min of covariates j */
     strcpy(pathtot,argv[1]);  
   }  
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    cptcoveff=0; 
   /*cygwin_split_path(pathtot,path,optionfile);   
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    for (k=-1; k < maxncov; k++) Ndum[k]=0;
   /* cutv(path,optionfile,pathtot,'\\');*/    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    /* Loop on covariates without age and products */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
   chdir(path);      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
   replace(pathc,path);                                 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
 /*-------- arguments in the command line --------*/                                      * If product of Vn*Vm, still boolean *:
                                       * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
   strcpy(fileres,"r");                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
   strcat(fileres, optionfilefiname);        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
   strcat(fileres,".txt");    /* Other files have txt extension */                                        modality of the nth covariate of individual i. */
         if (ij > modmaxcovj)
   /*---------arguments file --------*/          modmaxcovj=ij; 
         else if (ij < modmincovj) 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          modmincovj=ij; 
     printf("Problem with optionfile %s\n",optionfile);        if ((ij < -1) && (ij > NCOVMAX)){
     goto end;          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   }          exit(1);
         }else
   strcpy(filereso,"o");        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
   strcat(filereso,fileres);        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   if((ficparo=fopen(filereso,"w"))==NULL) {        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        /* getting the maximum value of the modality of the covariate
   }           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
            female is 1, then modmaxcovj=1.*/
   /* Reads comments: lines beginning with '#' */      }
   while((c=getc(ficpar))=='#' && c!= EOF){      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
     ungetc(c,ficpar);      cptcode=modmaxcovj;
     fgets(line, MAXLINE, ficpar);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
     puts(line);     /*for (i=0; i<=cptcode; i++) {*/
     fputs(line,ficparo);      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
   }        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
   ungetc(c,ficpar);        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        }
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
   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);           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
 while((c=getc(ficpar))=='#' && c!= EOF){      } /* Ndum[-1] number of undefined modalities */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
     puts(line);      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
     fputs(line,ficparo);      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
   }         modmincovj=3; modmaxcovj = 7;
   ungetc(c,ficpar);         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
           which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
             variables V1_1 and V1_2.
   covar=matrix(0,NCOVMAX,1,n);         nbcode[Tvar[j]][ij]=k;
   cptcovn=0;         nbcode[Tvar[j]][1]=0;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;         nbcode[Tvar[j]][2]=1;
          nbcode[Tvar[j]][3]=2;
   ncovmodel=2+cptcovn;      */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      ij=1; /* ij is similar to i but can jumps over null modalities */
        for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
   /* Read guess parameters */        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
   /* Reads comments: lines beginning with '#' */          /*recode from 0 */
   while((c=getc(ficpar))=='#' && c!= EOF){          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
     ungetc(c,ficpar);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
     fgets(line, MAXLINE, ficpar);                                       k is a modality. If we have model=V1+V1*sex 
     puts(line);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     fputs(line,ficparo);            ij++;
   }          }
   ungetc(c,ficpar);          if (ij > ncodemax[j]) break; 
          }  /* end of loop on */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      } /* end of loop on modality */ 
     for(i=1; i <=nlstate; i++)    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     for(j=1; j <=nlstate+ndeath-1; j++){    
       fscanf(ficpar,"%1d%1d",&i1,&j1);   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
       fprintf(ficparo,"%1d%1d",i1,j1);    
       printf("%1d%1d",i,j);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
       for(k=1; k<=ncovmodel;k++){     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
         fscanf(ficpar," %lf",&param[i][j][k]);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
         printf(" %lf",param[i][j][k]);     Ndum[ij]++; 
         fprintf(ficparo," %lf",param[i][j][k]);   } 
       }  
       fscanf(ficpar,"\n");   ij=1;
       printf("\n");   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
       fprintf(ficparo,"\n");     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
     }     if((Ndum[i]!=0) && (i<=ncovcol)){
         /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;       Tvaraff[ij]=i; /*For printing (unclear) */
        ij++;
   p=param[1][1];     }else
           Tvaraff[ij]=0;
   /* Reads comments: lines beginning with '#' */   }
   while((c=getc(ficpar))=='#' && c!= EOF){   ij--;
     ungetc(c,ficpar);   cptcoveff=ij; /*Number of total covariates*/
     fgets(line, MAXLINE, ficpar);  
     puts(line);  }
     fputs(line,ficparo);  
   }  
   ungetc(c,ficpar);  /*********** Health Expectancies ****************/
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){  {
     for(j=1; j <=nlstate+ndeath-1; j++){    /* Health expectancies, no variances */
       fscanf(ficpar,"%1d%1d",&i1,&j1);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
       printf("%1d%1d",i,j);    int nhstepma, nstepma; /* Decreasing with age */
       fprintf(ficparo,"%1d%1d",i1,j1);    double age, agelim, hf;
       for(k=1; k<=ncovmodel;k++){    double ***p3mat;
         fscanf(ficpar,"%le",&delti3[i][j][k]);    double eip;
         printf(" %le",delti3[i][j][k]);  
         fprintf(ficparo," %le",delti3[i][j][k]);    pstamp(ficreseij);
       }    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
       fscanf(ficpar,"\n");    fprintf(ficreseij,"# Age");
       printf("\n");    for(i=1; i<=nlstate;i++){
       fprintf(ficparo,"\n");      for(j=1; j<=nlstate;j++){
     }        fprintf(ficreseij," e%1d%1d ",i,j);
   }      }
   delti=delti3[1][1];      fprintf(ficreseij," e%1d. ",i);
      }
   /* Reads comments: lines beginning with '#' */    fprintf(ficreseij,"\n");
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    if(estepm < stepm){
     puts(line);      printf ("Problem %d lower than %d\n",estepm, stepm);
     fputs(line,ficparo);    }
   }    else  hstepm=estepm;   
   ungetc(c,ficpar);    /* We compute the life expectancy from trapezoids spaced every estepm months
       * This is mainly to measure the difference between two models: for example
   matcov=matrix(1,npar,1,npar);     * if stepm=24 months pijx are given only every 2 years and by summing them
   for(i=1; i <=npar; i++){     * we are calculating an estimate of the Life Expectancy assuming a linear 
     fscanf(ficpar,"%s",&str);     * progression in between and thus overestimating or underestimating according
     printf("%s",str);     * to the curvature of the survival function. If, for the same date, we 
     fprintf(ficparo,"%s",str);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     for(j=1; j <=i; j++){     * to compare the new estimate of Life expectancy with the same linear 
       fscanf(ficpar," %le",&matcov[i][j]);     * hypothesis. A more precise result, taking into account a more precise
       printf(" %.5le",matcov[i][j]);     * curvature will be obtained if estepm is as small as stepm. */
       fprintf(ficparo," %.5le",matcov[i][j]);  
     }    /* For example we decided to compute the life expectancy with the smallest unit */
     fscanf(ficpar,"\n");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     printf("\n");       nhstepm is the number of hstepm from age to agelim 
     fprintf(ficparo,"\n");       nstepm is the number of stepm from age to agelin. 
   }       Look at hpijx to understand the reason of that which relies in memory size
   for(i=1; i <=npar; i++)       and note for a fixed period like estepm months */
     for(j=i+1;j<=npar;j++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       matcov[i][j]=matcov[j][i];       survival function given by stepm (the optimization length). Unfortunately it
           means that if the survival funtion is printed only each two years of age and if
   printf("\n");       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.
     */
     /*-------- Rewriting paramater file ----------*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      strcpy(rfileres,"r");    /* "Rparameterfile */  
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    agelim=AGESUP;
      strcat(rfileres,".");    /* */    /* If stepm=6 months */
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     if((ficres =fopen(rfileres,"w"))==NULL) {         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      
     }  /* nhstepm age range expressed in number of stepm */
     fprintf(ficres,"#%s\n",version);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
        /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /*-------- data file ----------*/    /* if (stepm >= YEARM) hstepm=1;*/
     if((fic=fopen(datafile,"r"))==NULL)    {    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       printf("Problem with datafile: %s\n", datafile);goto end;    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }  
     for (age=bage; age<=fage; age ++){ 
     n= lastobs;      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     severity = vector(1,maxwav);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     outcome=imatrix(1,maxwav+1,1,n);      /* if (stepm >= YEARM) hstepm=1;*/
     num=ivector(1,n);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     moisnais=vector(1,n);  
     annais=vector(1,n);      /* If stepm=6 months */
     moisdc=vector(1,n);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     andc=vector(1,n);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     agedc=vector(1,n);      
     cod=ivector(1,n);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     weight=vector(1,n);      
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     mint=matrix(1,maxwav,1,n);      
     anint=matrix(1,maxwav,1,n);      printf("%d|",(int)age);fflush(stdout);
     s=imatrix(1,maxwav+1,1,n);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     adl=imatrix(1,maxwav+1,1,n);          
     tab=ivector(1,NCOVMAX);      /* Computing expectancies */
     ncodemax=ivector(1,8);      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
     i=1;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     while (fgets(line, MAXLINE, fic) != NULL)    {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       if ((i >= firstobs) && (i <=lastobs)) {            
                    /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          }
           strcpy(line,stra);  
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficreseij,"%3.0f",age );
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      for(i=1; i<=nlstate;i++){
         }        eip=0;
                for(j=1; j<=nlstate;j++){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          eip +=eij[i][j][(int)age];
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficreseij,"%9.4f", eip );
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      }
       fprintf(ficreseij,"\n");
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      
         for (j=ncovcol;j>=1;j--){    }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    printf("\n");
         num[i]=atol(stra);    fprintf(ficlog,"\n");
            
         /*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;}*/  
   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[] )
         i=i+1;  
       }  {
     }    /* Covariances of health expectancies eij and of total life expectancies according
     /* printf("ii=%d", ij);     to initial status i, ei. .
        scanf("%d",i);*/    */
   imx=i-1; /* Number of individuals */    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
   /* for (i=1; i<=imx; i++){    double age, agelim, hf;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    double ***p3matp, ***p3matm, ***varhe;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    double **dnewm,**doldm;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    double *xp, *xm;
     }*/    double **gp, **gm;
    /*  for (i=1; i<=imx; i++){    double ***gradg, ***trgradg;
      if (s[4][i]==9)  s[4][i]=-1;    int theta;
      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]));}*/  
      double eip, vip;
    
   /* Calculation of the number of parameter from char model*/    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   Tvar=ivector(1,15);    xp=vector(1,npar);
   Tprod=ivector(1,15);    xm=vector(1,npar);
   Tvaraff=ivector(1,15);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   Tvard=imatrix(1,15,1,2);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   Tage=ivector(1,15);          
        pstamp(ficresstdeij);
   if (strlen(model) >1){    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     j=0, j1=0, k1=1, k2=1;    fprintf(ficresstdeij,"# Age");
     j=nbocc(model,'+');    for(i=1; i<=nlstate;i++){
     j1=nbocc(model,'*');      for(j=1; j<=nlstate;j++)
     cptcovn=j+1;        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
     cptcovprod=j1;      fprintf(ficresstdeij," e%1d. ",i);
        }
     strcpy(modelsav,model);    fprintf(ficresstdeij,"\n");
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  
       printf("Error. Non available option model=%s ",model);    pstamp(ficrescveij);
       goto end;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     }    fprintf(ficrescveij,"# Age");
        for(i=1; i<=nlstate;i++)
     for(i=(j+1); i>=1;i--){      for(j=1; j<=nlstate;j++){
       cutv(stra,strb,modelsav,'+');        cptj= (j-1)*nlstate+i;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        for(i2=1; i2<=nlstate;i2++)
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          for(j2=1; j2<=nlstate;j2++){
       /*scanf("%d",i);*/            cptj2= (j2-1)*nlstate+i2;
       if (strchr(strb,'*')) {            if(cptj2 <= cptj)
         cutv(strd,strc,strb,'*');              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
         if (strcmp(strc,"age")==0) {          }
           cptcovprod--;      }
           cutv(strb,stre,strd,'V');    fprintf(ficrescveij,"\n");
           Tvar[i]=atoi(stre);    
           cptcovage++;    if(estepm < stepm){
             Tage[cptcovage]=i;      printf ("Problem %d lower than %d\n",estepm, stepm);
             /*printf("stre=%s ", stre);*/    }
         }    else  hstepm=estepm;   
         else if (strcmp(strd,"age")==0) {    /* We compute the life expectancy from trapezoids spaced every estepm months
           cptcovprod--;     * This is mainly to measure the difference between two models: for example
           cutv(strb,stre,strc,'V');     * if stepm=24 months pijx are given only every 2 years and by summing them
           Tvar[i]=atoi(stre);     * we are calculating an estimate of the Life Expectancy assuming a linear 
           cptcovage++;     * progression in between and thus overestimating or underestimating according
           Tage[cptcovage]=i;     * 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
         else {     * to compare the new estimate of Life expectancy with the same linear 
           cutv(strb,stre,strc,'V');     * hypothesis. A more precise result, taking into account a more precise
           Tvar[i]=ncovcol+k1;     * curvature will be obtained if estepm is as small as stepm. */
           cutv(strb,strc,strd,'V');  
           Tprod[k1]=i;    /* For example we decided to compute the life expectancy with the smallest unit */
           Tvard[k1][1]=atoi(strc);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           Tvard[k1][2]=atoi(stre);       nhstepm is the number of hstepm from age to agelim 
           Tvar[cptcovn+k2]=Tvard[k1][1];       nstepm is the number of stepm from age to agelin. 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];       Look at hpijx to understand the reason of that which relies in memory size
           for (k=1; k<=lastobs;k++)       and note for a fixed period like estepm months */
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           k1++;       survival function given by stepm (the optimization length). Unfortunately it
           k2=k2+2;       means that if the survival funtion is printed only each two years of age and if
         }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       }       results. So we changed our mind and took the option of the best precision.
       else {    */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');    /* If stepm=6 months */
       Tvar[i]=atoi(strc);    /* nhstepm age range expressed in number of stepm */
       }    agelim=AGESUP;
       strcpy(modelsav,stra);      nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         scanf("%d",i);*/    /* if (stepm >= YEARM) hstepm=1;*/
     }    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 }    
      p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("cptcovprod=%d ", cptcovprod);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   scanf("%d ",i);*/    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     fclose(fic);    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/    for (age=bage; age<=fage; age ++){ 
       for(i=1;i<=n;i++) weight[i]=1.0;      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /*-calculation of age at interview from date of interview and age at death -*/      /* if (stepm >= YEARM) hstepm=1;*/
     agev=matrix(1,maxwav,1,imx);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
     for (i=1; i<=imx; i++) {      /* If stepm=6 months */
       for(m=2; (m<= maxwav); m++) {      /* Computed by stepm unit matrices, product of hstepma matrices, stored
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
          anint[m][i]=9999;      
          s[m][i]=-1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        }  
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;      /* Computing  Variances of health expectancies */
       }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     }         decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
     for (i=1; i<=imx; i++)  {        for(i=1; i<=npar; i++){ 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for(m=1; (m<= maxwav); m++){          xm[i] = x[i] - (i==theta ?delti[theta]:0);
         if(s[m][i] >0){        }
           if (s[m][i] >= nlstate+1) {        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
             if(agedc[i]>0)        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
               if(moisdc[i]!=99 && andc[i]!=9999)    
                 agev[m][i]=agedc[i];        for(j=1; j<= nlstate; j++){
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/          for(i=1; i<=nlstate; i++){
            else {            for(h=0; h<=nhstepm-1; h++){
               if (andc[i]!=9999){              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
               agev[m][i]=-1;            }
               }          }
             }        }
           }       
           else if(s[m][i] !=9){ /* Should no more exist */        for(ij=1; ij<= nlstate*nlstate; ij++)
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          for(h=0; h<=nhstepm-1; h++){
             if(mint[m][i]==99 || anint[m][i]==9999)            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
               agev[m][i]=1;          }
             else if(agev[m][i] <agemin){      }/* End theta */
               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);*/      
             }      for(h=0; h<=nhstepm-1; h++)
             else if(agev[m][i] >agemax){        for(j=1; j<=nlstate*nlstate;j++)
               agemax=agev[m][i];          for(theta=1; theta <=npar; theta++)
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            trgradg[h][j][theta]=gradg[h][theta][j];
             }      
             /*agev[m][i]=anint[m][i]-annais[i];*/  
             /*   agev[m][i] = age[i]+2*m;*/       for(ij=1;ij<=nlstate*nlstate;ij++)
           }        for(ji=1;ji<=nlstate*nlstate;ji++)
           else { /* =9 */          varhe[ij][ji][(int)age] =0.;
             agev[m][i]=1;  
             s[m][i]=-1;       printf("%d|",(int)age);fflush(stdout);
           }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         }       for(h=0;h<=nhstepm-1;h++){
         else /*= 0 Unknown */        for(k=0;k<=nhstepm-1;k++){
           agev[m][i]=1;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
              for(ij=1;ij<=nlstate*nlstate;ij++)
     }            for(ji=1;ji<=nlstate*nlstate;ji++)
     for (i=1; i<=imx; i++)  {              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       for(m=1; (m<= maxwav); m++){        }
         if (s[m][i] > (nlstate+ndeath)) {      }
           printf("Error: Wrong value in nlstate or ndeath\n");    
           goto end;      /* Computing expectancies */
         }      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       }      for(i=1; i<=nlstate;i++)
     }        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
     free_vector(severity,1,maxwav);            /* 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]);*/
     free_imatrix(outcome,1,maxwav+1,1,n);  
     free_vector(moisnais,1,n);          }
     free_vector(annais,1,n);  
     /* free_matrix(mint,1,maxwav,1,n);      fprintf(ficresstdeij,"%3.0f",age );
        free_matrix(anint,1,maxwav,1,n);*/      for(i=1; i<=nlstate;i++){
     free_vector(moisdc,1,n);        eip=0.;
     free_vector(andc,1,n);        vip=0.;
         for(j=1; j<=nlstate;j++){
              eip += eij[i][j][(int)age];
     wav=ivector(1,imx);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
            }
     /* Concatenates waves */        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      }
       fprintf(ficresstdeij,"\n");
   
       Tcode=ivector(1,100);      fprintf(ficrescveij,"%3.0f",age );
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      for(i=1; i<=nlstate;i++)
       ncodemax[1]=1;        for(j=1; j<=nlstate;j++){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          cptj= (j-1)*nlstate+i;
                for(i2=1; i2<=nlstate;i2++)
    codtab=imatrix(1,100,1,10);            for(j2=1; j2<=nlstate;j2++){
    h=0;              cptj2= (j2-1)*nlstate+i2;
    m=pow(2,cptcoveff);              if(cptj2 <= cptj)
                  fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
    for(k=1;k<=cptcoveff; k++){            }
      for(i=1; i <=(m/pow(2,k));i++){        }
        for(j=1; j <= ncodemax[k]; j++){      fprintf(ficrescveij,"\n");
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){     
            h++;    }
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
          }    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
        }    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
      }    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    }    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    printf("\n");
       codtab[1][2]=1;codtab[2][2]=2; */    fprintf(ficlog,"\n");
    /* for(i=1; i <=m ;i++){  
       for(k=1; k <=cptcovn; k++){    free_vector(xm,1,npar);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    free_vector(xp,1,npar);
       }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       printf("\n");    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       scanf("%d",i);*/  }
      
    /* Calculates basic frequencies. Computes observed prevalence at single age  /************ Variance ******************/
        and prints on file fileres'p'. */  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 of health expectancies */
        /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* double **newm;*/
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double **dnewm,**doldm;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double **dnewmp,**doldmp;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int i, j, nhstepm, hstepm, h, nstepm ;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    int k, cptcode;
          double *xp;
     /* For Powell, parameters are in a vector p[] starting at p[1]    double **gp, **gm;  /* for var eij */
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    double ***gradg, ***trgradg; /*for var eij */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     if(mle==1){    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    double ***p3mat;
     }    double age,agelim, hf;
        double ***mobaverage;
     /*--------- results files --------------*/    int theta;
     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);    char digit[4];
      char digitp[25];
   
    jk=1;    char fileresprobmorprev[FILENAMELENGTH];
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    if(popbased==1){
    for(i=1,jk=1; i <=nlstate; i++){      if(mobilav!=0)
      for(k=1; k <=(nlstate+ndeath); k++){        strcpy(digitp,"-populbased-mobilav-");
        if (k != i)      else strcpy(digitp,"-populbased-nomobil-");
          {    }
            printf("%d%d ",i,k);    else 
            fprintf(ficres,"%1d%1d ",i,k);      strcpy(digitp,"-stablbased-");
            for(j=1; j <=ncovmodel; j++){  
              printf("%f ",p[jk]);    if (mobilav!=0) {
              fprintf(ficres,"%f ",p[jk]);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
              jk++;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
            }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
            printf("\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
            fprintf(ficres,"\n");      }
          }    }
      }  
    }    strcpy(fileresprobmorprev,"prmorprev"); 
  if(mle==1){    sprintf(digit,"%-d",ij);
     /* Computing hessian and covariance matrix */    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     ftolhess=ftol; /* Usually correct */    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     hesscov(matcov, p, npar, delti, ftolhess, func);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
  }    strcat(fileresprobmorprev,fileres);
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     printf("# Scales (for hessian or gradient estimation)\n");      printf("Problem with resultfile: %s\n", fileresprobmorprev);
      for(i=1,jk=1; i <=nlstate; i++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       for(j=1; j <=nlstate+ndeath; j++){    }
         if (j!=i) {    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           fprintf(ficres,"%1d%1d",i,j);   
           printf("%1d%1d",i,j);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           for(k=1; k<=ncovmodel;k++){    pstamp(ficresprobmorprev);
             printf(" %.5e",delti[jk]);    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
             fprintf(ficres," %.5e",delti[jk]);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
             jk++;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           }      fprintf(ficresprobmorprev," p.%-d SE",j);
           printf("\n");      for(i=1; i<=nlstate;i++)
           fprintf(ficres,"\n");        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
         }    }  
       }    fprintf(ficresprobmorprev,"\n");
      }    fprintf(ficgp,"\n# Routine varevsij");
        /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     k=1;    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(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");    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");  /*   } */
     for(i=1;i<=npar;i++){    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       /*  if (k>nlstate) k=1;    pstamp(ficresvij);
       i1=(i-1)/(ncovmodel*nlstate)+1;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    if(popbased==1)
       printf("%s%d%d",alph[k],i1,tab[i]);*/      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);
       fprintf(ficres,"%3d",i);    else
       printf("%3d",i);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
       for(j=1; j<=i;j++){    fprintf(ficresvij,"# Age");
         fprintf(ficres," %.5e",matcov[i][j]);    for(i=1; i<=nlstate;i++)
         printf(" %.5e",matcov[i][j]);      for(j=1; j<=nlstate;j++)
       }        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
       fprintf(ficres,"\n");    fprintf(ficresvij,"\n");
       printf("\n");  
       k++;    xp=vector(1,npar);
     }    dnewm=matrix(1,nlstate,1,npar);
        doldm=matrix(1,nlstate,1,nlstate);
     while((c=getc(ficpar))=='#' && c!= EOF){    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       ungetc(c,ficpar);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       fgets(line, MAXLINE, ficpar);  
       puts(line);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       fputs(line,ficparo);    gpp=vector(nlstate+1,nlstate+ndeath);
     }    gmp=vector(nlstate+1,nlstate+ndeath);
     ungetc(c,ficpar);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     estepm=0;    
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    if(estepm < stepm){
     if (estepm==0 || estepm < stepm) estepm=stepm;      printf ("Problem %d lower than %d\n",estepm, stepm);
     if (fage <= 2) {    }
       bage = ageminpar;    else  hstepm=estepm;   
       fage = agemaxpar;    /* 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 
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");       nstepm is the number of stepm from age to agelin. 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);       Look at function hpijx to understand why (it is linked to memory size questions) */
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         survival function given by stepm (the optimization length). Unfortunately it
     while((c=getc(ficpar))=='#' && c!= EOF){       means that if the survival funtion is printed every two years of age and if
     ungetc(c,ficpar);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     fgets(line, MAXLINE, ficpar);       results. So we changed our mind and took the option of the best precision.
     puts(line);    */
     fputs(line,ficparo);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }    agelim = AGESUP;
   ungetc(c,ficpar);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
            gp=matrix(0,nhstepm,1,nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){      gm=matrix(0,nhstepm,1,nlstate);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     puts(line);      for(theta=1; theta <=npar; theta++){
     fputs(line,ficparo);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   ungetc(c,ficpar);        }
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;  
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        if (popbased==1) {
           if(mobilav ==0){
   fscanf(ficpar,"pop_based=%d\n",&popbased);            for(i=1; i<=nlstate;i++)
   fprintf(ficparo,"pop_based=%d\n",popbased);                prlim[i][i]=probs[(int)age][i][ij];
   fprintf(ficres,"pop_based=%d\n",popbased);            }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){              prlim[i][i]=mobaverage[(int)age][i][ij];
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }
     puts(line);    
     fputs(line,ficparo);        for(j=1; j<= nlstate; j++){
   }          for(h=0; h<=nhstepm; h++){
   ungetc(c,ficpar);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          }
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        }
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
 while((c=getc(ficpar))=='#' && c!= EOF){        */
     ungetc(c,ficpar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     fgets(line, MAXLINE, ficpar);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     puts(line);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     fputs(line,ficparo);        }    
   }        /* end probability of death */
   ungetc(c,ficpar);  
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        if (popbased==1) {
           if(mobilav ==0){
 /*------------ gnuplot -------------*/            for(i=1; i<=nlstate;i++)
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);              prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
 /*------------ free_vector  -------------*/            for(i=1; i<=nlstate;i++)
  chdir(path);              prlim[i][i]=mobaverage[(int)age][i][ij];
            }
  free_ivector(wav,1,imx);        }
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
  free_ivector(num,1,n);          for(h=0; h<=nhstepm; h++){
  free_vector(agedc,1,n);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
  /*free_matrix(covar,1,NCOVMAX,1,n);*/              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
  fclose(ficparo);          }
  fclose(ficres);        }
         /* This for computing probability of death (h=1 means
 /*--------- index.htm --------*/           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gmp[j]=0.; i<= nlstate; i++)
   /*--------------- Prevalence limit --------------*/           gmp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
   strcpy(filerespl,"pl");        /* end probability of death */
   strcat(filerespl,fileres);  
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        for(j=1; j<= nlstate; j++) /* vareij */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          for(h=0; h<=nhstepm; h++){
   }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          }
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   fprintf(ficrespl,"\n");        }
    
   prlim=matrix(1,nlstate,1,nlstate);      } /* End theta */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(h=0; h<=nhstepm; h++) /* veij */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        for(j=1; j<=nlstate;j++)
   k=0;          for(theta=1; theta <=npar; theta++)
   agebase=ageminpar;            trgradg[h][j][theta]=gradg[h][theta][j];
   agelim=agemaxpar;  
   ftolpl=1.e-10;      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   i1=cptcoveff;        for(theta=1; theta <=npar; theta++)
   if (cptcovn < 1){i1=1;}          trgradgp[j][theta]=gradgp[theta][j];
     
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         k=k+1;      for(i=1;i<=nlstate;i++)
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        for(j=1;j<=nlstate;j++)
         fprintf(ficrespl,"\n#******");          vareij[i][j][(int)age] =0.;
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(h=0;h<=nhstepm;h++){
         fprintf(ficrespl,"******\n");        for(k=0;k<=nhstepm;k++){
                  matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         for (age=agebase; age<=agelim; age++){          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          for(i=1;i<=nlstate;i++)
           fprintf(ficrespl,"%.0f",age );            for(j=1;j<=nlstate;j++)
           for(i=1; i<=nlstate;i++)              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
           fprintf(ficrespl," %.5f", prlim[i][i]);        }
           fprintf(ficrespl,"\n");      }
         }    
       }      /* pptj */
     }      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   fclose(ficrespl);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
   /*------------- h Pij x at various ages ------------*/        for(i=nlstate+1;i<=nlstate+ndeath;i++)
            varppt[j][i]=doldmp[j][i];
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      /* end ppptj */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      /*  x centered again */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   printf("Computing pij: result on file '%s' \n", filerespij);   
        if (popbased==1) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;        if(mobilav ==0){
   /*if (stepm<=24) stepsize=2;*/          for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
   agelim=AGESUP;        }else{ /* mobilav */ 
   hstepm=stepsize*YEARM; /* Every year of age */          for(i=1; i<=nlstate;i++)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            prlim[i][i]=mobaverage[(int)age][i][ij];
          }
   k=0;      }
   for(cptcov=1;cptcov<=i1;cptcov++){               
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      /* This for computing probability of death (h=1 means
       k=k+1;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         fprintf(ficrespij,"\n#****** ");         as a weighted average of prlim.
         for(j=1;j<=cptcoveff;j++)      */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         fprintf(ficrespij,"******\n");        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
                  gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      }    
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      /* end probability of death */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           oldm=oldms;savm=savms;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
           fprintf(ficrespij,"# Age");        for(i=1; i<=nlstate;i++){
           for(i=1; i<=nlstate;i++)          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
             for(j=1; j<=nlstate+ndeath;j++)        }
               fprintf(ficrespij," %1d-%1d",i,j);      } 
           fprintf(ficrespij,"\n");      fprintf(ficresprobmorprev,"\n");
            for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      fprintf(ficresvij,"%.0f ",age );
             for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)        for(j=1; j<=nlstate;j++){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
             fprintf(ficrespij,"\n");        }
              }      fprintf(ficresvij,"\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      free_matrix(gp,0,nhstepm,1,nlstate);
           fprintf(ficrespij,"\n");      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 */
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
   fclose(ficrespij);    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");
   /*---------- Forecasting ------------------*/    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   if((stepm == 1) && (strcmp(model,".")==0)){    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  /*   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); */
   else{    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     erreur=108;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);    fprintf(ficgp,"\n 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);
   /*---------- Health expectancies and variances ------------*/  */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   strcpy(filerest,"t");    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {    free_vector(xp,1,npar);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    free_matrix(doldm,1,nlstate,1,nlstate);
   }    free_matrix(dnewm,1,nlstate,1,npar);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    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);
   strcpy(filerese,"e");    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcat(filerese,fileres);    fclose(ficresprobmorprev);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    fflush(ficgp);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    fflush(fichtm); 
   }  }  /* end varevsij */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
   /************ Variance of prevlim ******************/
  strcpy(fileresv,"v");  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[])
   strcat(fileresv,fileres);  {
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    /* Variance of prevalence limit */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   }    double **newm;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    double **dnewm,**doldm;
   calagedate=-1;    int i, j, nhstepm, hstepm;
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    int k, cptcode;
     double *xp;
   k=0;    double *gp, *gm;
   for(cptcov=1;cptcov<=i1;cptcov++){    double **gradg, **trgradg;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double age,agelim;
       k=k+1;    int theta;
       fprintf(ficrest,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    pstamp(ficresvpl);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
       fprintf(ficrest,"******\n");    fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
       fprintf(ficreseij,"\n#****** ");        fprintf(ficresvpl," %1d-%1d",i,i);
       for(j=1;j<=cptcoveff;j++)    fprintf(ficresvpl,"\n");
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
       fprintf(ficresvij,"\n#****** ");    doldm=matrix(1,nlstate,1,nlstate);
       for(j=1;j<=cptcoveff;j++)    
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    hstepm=1*YEARM; /* Every year of age */
       fprintf(ficresvij,"******\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       oldm=oldms;savm=savms;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);        if (stepm >= YEARM) hstepm=1;
        nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      gradg=matrix(1,npar,1,nlstate);
       oldm=oldms;savm=savms;      gp=vector(1,nlstate);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);      gm=vector(1,nlstate);
      
       for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        }
       fprintf(ficrest,"\n");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
       epj=vector(1,nlstate+1);          gp[i] = prlim[i][i];
       for(age=bage; age <=fage ;age++){      
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for(i=1; i<=npar; i++) /* Computes gradient */
         if (popbased==1) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           for(i=1; i<=nlstate;i++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             prlim[i][i]=probs[(int)age][i][k];        for(i=1;i<=nlstate;i++)
         }          gm[i] = prlim[i][i];
          
         fprintf(ficrest," %4.0f",age);        for(i=1;i<=nlstate;i++)
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      } /* End theta */
             epj[j] += prlim[i][i]*eij[i][j][(int)age];  
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/      trgradg =matrix(1,nlstate,1,npar);
           }  
           epj[nlstate+1] +=epj[j];      for(j=1; j<=nlstate;j++)
         }        for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
         for(i=1, vepp=0.;i <=nlstate;i++)  
           for(j=1;j <=nlstate;j++)      for(i=1;i<=nlstate;i++)
             vepp += vareij[i][j][(int)age];        varpl[i][(int)age] =0.;
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
         for(j=1;j <=nlstate;j++){      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));      for(i=1;i<=nlstate;i++)
         }        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
         fprintf(ficrest,"\n");  
       }      fprintf(ficresvpl,"%.0f ",age );
     }      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
 free_matrix(mint,1,maxwav,1,n);      fprintf(ficresvpl,"\n");
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      free_vector(gp,1,nlstate);
     free_vector(weight,1,n);      free_vector(gm,1,nlstate);
   fclose(ficreseij);      free_matrix(gradg,1,npar,1,nlstate);
   fclose(ficresvij);      free_matrix(trgradg,1,nlstate,1,npar);
   fclose(ficrest);    } /* End age */
   fclose(ficpar);  
   free_vector(epj,1,nlstate+1);    free_vector(xp,1,npar);
      free_matrix(doldm,1,nlstate,1,npar);
   /*------- Variance limit prevalence------*/      free_matrix(dnewm,1,nlstate,1,nlstate);
   
   strcpy(fileresvpl,"vpl");  }
   strcat(fileresvpl,fileres);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  /************ Variance of one-step probabilities  ******************/
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  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[])
     exit(0);  {
   }    int i, j=0,  i1, k1, l1, t, tj;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
   k=0;    int first=1, first1, first2;
   for(cptcov=1;cptcov<=i1;cptcov++){    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double **dnewm,**doldm;
       k=k+1;    double *xp;
       fprintf(ficresvpl,"\n#****** ");    double *gp, *gm;
       for(j=1;j<=cptcoveff;j++)    double **gradg, **trgradg;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double **mu;
       fprintf(ficresvpl,"******\n");    double age,agelim, cov[NCOVMAX+1];
          double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    int theta;
       oldm=oldms;savm=savms;    char fileresprob[FILENAMELENGTH];
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    char fileresprobcov[FILENAMELENGTH];
     }    char fileresprobcor[FILENAMELENGTH];
  }    double ***varpij;
   
   fclose(ficresvpl);    strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
   /*---------- End : free ----------------*/    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      printf("Problem with resultfile: %s\n", fileresprob);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    strcpy(fileresprobcov,"probcov"); 
      strcat(fileresprobcov,fileres);
      if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      printf("Problem with resultfile: %s\n", fileresprobcov);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    }
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    strcpy(fileresprobcor,"probcor"); 
      strcat(fileresprobcor,fileres);
   free_matrix(matcov,1,npar,1,npar);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   free_vector(delti,1,npar);      printf("Problem with resultfile: %s\n", fileresprobcor);
   free_matrix(agev,1,maxwav,1,imx);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   if(erreur >0)    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("End of Imach with error or warning %d\n",erreur);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   else   printf("End of Imach\n");    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    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);
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/    pstamp(ficresprob);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   /*------ End -----------*/    fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
  end:    fprintf(ficresprobcov,"# Age");
 #ifdef windows    pstamp(ficresprobcor);
   /* chdir(pathcd);*/    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
 #endif    fprintf(ficresprobcor,"# Age");
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/  
  /*system("cd ../gp37mgw");*/    for(i=1; i<=nlstate;i++)
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      for(j=1; j<=(nlstate+ndeath);j++){
  strcpy(plotcmd,GNUPLOTPROGRAM);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
  strcat(plotcmd," ");        fprintf(ficresprobcov," p%1d-%1d ",i,j);
  strcat(plotcmd,optionfilegnuplot);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
  system(plotcmd);      }  
    /* fprintf(ficresprob,"\n");
 #ifdef windows    fprintf(ficresprobcov,"\n");
   while (z[0] != 'q') {    fprintf(ficresprobcor,"\n");
     /* chdir(path); */   */
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    xp=vector(1,npar);
     scanf("%s",z);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     if (z[0] == 'c') system("./imach");    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     else if (z[0] == 'e') system(optionfilehtm);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     else if (z[0] == 'g') system(plotcmd);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     else if (z[0] == 'q') exit(0);    first=1;
   }    fprintf(ficgp,"\n# Routine varprob");
 #endif    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 with errno=%s\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile %s with errno=%s\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot command %s\n"plotcmd);
       printf("\n Trying on same directory\n");
       sprintf(plotcmd,"./gnuplot %s", optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s\n", plotcmd);
     }
     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.1.44  
changed lines
  Added in v.1.150


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