Diff for /imach/src/imach.c between versions 1.46 and 1.145

version 1.46, 2002/05/30 17:44:35 version 1.145, 2014/06/10 21:23:15
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.145  2014/06/10 21:23:15  brouard
      Summary: Debugging with valgrind
   This program computes Healthy Life Expectancies from    Author: Nicolas Brouard
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Lot of changes in order to output the results with some covariates
   interviewed on their health status or degree of disability (in the    After the Edimburgh REVES conference 2014, it seems mandatory to
   case of a health survey which is our main interest) -2- at least a    improve the code.
   second wave of interviews ("longitudinal") which measure each change    No more memory valgrind error but a lot has to be done in order to
   (if any) in individual health status.  Health expectancies are    continue the work of splitting the code into subroutines.
   computed from the time spent in each health state according to a    Also, decodemodel has been improved. Tricode is still not
   model. More health states you consider, more time is necessary to reach the    optimal. nbcode should be improved. Documentation has been added in
   Maximum Likelihood of the parameters involved in the model.  The    the source code.
   simplest model is the multinomial logistic model where pij is the  
   probability to be observed in state j at the second wave    Revision 1.143  2014/01/26 09:45:38  brouard
   conditional to be observed in state i at the first wave. Therefore    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   complex model than "constant and age", you should modify the program    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.142  2014/01/26 03:57:36  brouard
   convergence.    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   
   The advantage of this computer programme, compared to a simple    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.141  2014/01/26 02:42:01  brouard
   intermediate interview, the information is lost, but taken into    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   account using an interpolation or extrapolation.    
     Revision 1.140  2011/09/02 10:37:54  brouard
   hPijx is the probability to be observed in state i at age x+h    Summary: times.h is ok with mingw32 now.
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.139  2010/06/14 07:50:17  brouard
   states. This elementary transition (by month or quarter trimester,    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   semester or year) is model as a multinomial logistic.  The hPx    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.138  2010/04/30 18:19:40  brouard
   hPijx.    *** empty log message ***
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.137  2010/04/29 18:11:38  brouard
   of the life expectancies. It also computes the prevalence limits.    (Module): Checking covariates for more complex models
      than V1+V2. A lot of change to be done. Unstable.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.136  2010/04/26 20:30:53  brouard
   This software have been partly granted by Euro-REVES, a concerted action    (Module): merging some libgsl code. Fixing computation
   from the European Union.    of likelione (using inter/intrapolation if mle = 0) in order to
   It is copyrighted identically to a GNU software product, ie programme and    get same likelihood as if mle=1.
   software can be distributed freely for non commercial use. Latest version    Some cleaning of code and comments added.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.135  2009/10/29 15:33:14  brouard
      (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #include <math.h>  
 #include <stdio.h>    Revision 1.134  2009/10/29 13:18:53  brouard
 #include <stdlib.h>    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #include <unistd.h>  
     Revision 1.133  2009/07/06 10:21:25  brouard
 #define MAXLINE 256    just nforces
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.132  2009/07/06 08:22:05  brouard
 #define FILENAMELENGTH 80    Many tings
 /*#define DEBUG*/  
 #define windows    Revision 1.131  2009/06/20 16:22:47  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Some dimensions resccaled
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.130  2009/05/26 06:44:34  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    (Module): Max Covariate is now set to 20 instead of 8. A
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    lot of cleaning with variables initialized to 0. Trying to make
     V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.129  2007/08/31 13:49:27  lievre
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.128  2006/06/30 13:02:05  brouard
 #define YEARM 12. /* Number of months per year */    (Module): Clarifications on computing e.j
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 int erreur; /* Error number */    loop. Now we define nhstepma in the age loop.
 int nvar;    (Module): In order to speed up (in case of numerous covariates) we
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    compute health expectancies (without variances) in a first step
 int npar=NPARMAX;    and then all the health expectancies with variances or standard
 int nlstate=2; /* Number of live states */    deviation (needs data from the Hessian matrices) which slows the
 int ndeath=1; /* Number of dead states */    computation.
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    In the future we should be able to stop the program is only health
 int popbased=0;    expectancies and graph are needed without standard deviations.
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.126  2006/04/28 17:23:28  brouard
 int maxwav; /* Maxim number of waves */    (Module): Yes the sum of survivors was wrong since
 int jmin, jmax; /* min, max spacing between 2 waves */    imach-114 because nhstepm was no more computed in the age
 int mle, weightopt;    loop. Now we define nhstepma in the age loop.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Version 0.98h
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.125  2006/04/04 15:20:31  lievre
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Errors in calculation of health expectancies. Age was not initialized.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Forecasting file added.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    Revision 1.124  2006/03/22 17:13:53  lievre
 FILE *ficreseij;    Parameters are printed with %lf instead of %f (more numbers after the comma).
   char filerese[FILENAMELENGTH];    The log-likelihood is printed in the log file
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.123  2006/03/20 10:52:43  brouard
  FILE  *ficresvpl;    * imach.c (Module): <title> changed, corresponds to .htm file
   char fileresvpl[FILENAMELENGTH];    name. <head> headers where missing.
   
 #define NR_END 1    * imach.c (Module): Weights can have a decimal point as for
 #define FREE_ARG char*    English (a comma might work with a correct LC_NUMERIC environment,
 #define FTOL 1.0e-10    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 #define NRANSI    1.
 #define ITMAX 200    Version 0.98g
   
 #define TOL 2.0e-4    Revision 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
 #define CGOLD 0.3819660    English (a comma might work with a correct LC_NUMERIC environment,
 #define ZEPS 1.0e-10    otherwise the weight is truncated).
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Modification of warning when the covariates values are not 0 or
     1.
 #define GOLD 1.618034    Version 0.98g
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.121  2006/03/16 17:45:01  lievre
     * imach.c (Module): Comments concerning covariates added
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    * imach.c (Module): refinements in the computation of lli if
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    status=-2 in order to have more reliable computation if stepm is
      not 1 month. Version 0.98f
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
 static double sqrarg;    status=-2 in order to have more reliable computation if stepm is
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    not 1 month. Version 0.98f
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.119  2006/03/15 17:42:26  brouard
 int imx;    (Module): Bug if status = -2, the loglikelihood was
 int stepm;    computed as likelihood omitting the logarithm. Version O.98e
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.118  2006/03/14 18:20:07  brouard
 int estepm;    (Module): varevsij Comments added explaining the second
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int m,nb;    (Module): Function pstamp added
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (Module): Version 0.98d
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.117  2006/03/14 17:16:22  brouard
 double dateintmean=0;    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
 double *weight;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int **s; /* Status */    (Module): Function pstamp added
 double *agedc, **covar, idx;    (Module): Version 0.98d
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.116  2006/03/06 10:29:27  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): Variance-covariance wrong links and
 double ftolhess; /* Tolerance for computing hessian */    varian-covariance of ej. is needed (Saito).
   
 /**************** split *************************/    Revision 1.115  2006/02/27 12:17:45  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    (Module): One freematrix added in mlikeli! 0.98c
 {  
    char *s;                             /* pointer */    Revision 1.114  2006/02/26 12:57:58  brouard
    int  l1, l2;                         /* length counters */    (Module): Some improvements in processing parameter
     filename with strsep.
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.113  2006/02/24 14:20:24  brouard
 #ifdef windows    (Module): Memory leaks checks with valgrind and:
    s = strrchr( path, '\\' );           /* find last / */    datafile was not closed, some imatrix were not freed and on matrix
 #else    allocation too.
    s = strrchr( path, '/' );            /* find last / */  
 #endif    Revision 1.112  2006/01/30 09:55:26  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
       if ( getwd( dirc ) == NULL ) {    (Module): Comments can be added in data file. Missing date values
 #else    can be a simple dot '.'.
       extern char       *getcwd( );  
     Revision 1.110  2006/01/25 00:51:50  brouard
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    (Module): Lots of cleaning and bugs added (Gompertz)
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.109  2006/01/24 19:37:15  brouard
       }    (Module): Comments (lines starting with a #) are allowed in data.
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.108  2006/01/19 18:05:42  lievre
       s++;                              /* after this, the filename */    Gnuplot problem appeared...
       l2 = strlen( s );                 /* length of filename */    To be fixed
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.107  2006/01/19 16:20:37  brouard
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Test existence of gnuplot in imach path
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.106  2006/01/19 13:24:36  brouard
    l1 = strlen( dirc );                 /* length of directory */    Some cleaning and links added in html output
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.105  2006/01/05 20:23:19  lievre
 #else    *** empty log message ***
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.104  2005/09/30 16:11:43  lievre
    s = strrchr( name, '.' );            /* find last / */    (Module): sump fixed, loop imx fixed, and simplifications.
    s++;    (Module): If the status is missing at the last wave but we know
    strcpy(ext,s);                       /* save extension */    that the person is alive, then we can code his/her status as -2
    l1= strlen( name);    (instead of missing=-1 in earlier versions) and his/her
    l2= strlen( s)+1;    contributions to the likelihood is 1 - Prob of dying from last
    strncpy( finame, name, l1-l2);    health status (= 1-p13= p11+p12 in the easiest case of somebody in
    finame[l1-l2]= 0;    the healthy state at last known wave). Version is 0.98
    return( 0 );                         /* we're done */  
 }    Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
   
 /******************************************/    Revision 1.102  2004/09/15 17:31:30  brouard
     Add the possibility to read data file including tab characters.
 void replace(char *s, char*t)  
 {    Revision 1.101  2004/09/15 10:38:38  brouard
   int i;    Fix on curr_time
   int lg=20;  
   i=0;    Revision 1.100  2004/07/12 18:29:06  brouard
   lg=strlen(t);    Add version for Mac OS X. Just define UNIX in Makefile
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.99  2004/06/05 08:57:40  brouard
     if (t[i]== '\\') s[i]='/';    *** empty log message ***
   }  
 }    Revision 1.98  2004/05/16 15:05:56  brouard
     New version 0.97 . First attempt to estimate force of mortality
 int nbocc(char *s, char occ)    directly from the data i.e. without the need of knowing the health
 {    state at each age, but using a Gompertz model: log u =a + b*age .
   int i,j=0;    This is the basic analysis of mortality and should be done before any
   int lg=20;    other analysis, in order to test if the mortality estimated from the
   i=0;    cross-longitudinal survey is different from the mortality estimated
   lg=strlen(s);    from other sources like vital statistic data.
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;    The same imach parameter file can be used but the option for mle should be -3.
   }  
   return j;    Agnès, who wrote this part of the code, tried to keep most of the
 }    former routines in order to include the new code within the former code.
   
 void cutv(char *u,char *v, char*t, char occ)    The output is very simple: only an estimate of the intercept and of
 {    the slope with 95% confident intervals.
   int i,lg,j,p=0;  
   i=0;    Current limitations:
   for(j=0; j<=strlen(t)-1; j++) {    A) Even if you enter covariates, i.e. with the
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    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.
   
   lg=strlen(t);    Revision 1.97  2004/02/20 13:25:42  lievre
   for(j=0; j<p; j++) {    Version 0.96d. Population forecasting command line is (temporarily)
     (u[j] = t[j]);    suppressed.
   }  
      u[p]='\0';    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
    for(j=0; j<= lg; j++) {    rewritten within the same printf. Workaround: many printfs.
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.95  2003/07/08 07:54:34  brouard
 }    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 /********************** nrerror ********************/    matrix (cov(a12,c31) instead of numbers.
   
 void nrerror(char error_text[])    Revision 1.94  2003/06/27 13:00:02  brouard
 {    Just cleaning
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.93  2003/06/25 16:33:55  brouard
   exit(1);    (Module): On windows (cygwin) function asctime_r doesn't
 }    exist so I changed back to asctime which exists.
 /*********************** vector *******************/    (Module): Version 0.96b
 double *vector(int nl, int nh)  
 {    Revision 1.92  2003/06/25 16:30:45  brouard
   double *v;    (Module): On windows (cygwin) function asctime_r doesn't
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    exist so I changed back to asctime which exists.
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.91  2003/06/25 15:30:29  brouard
 }    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
 /************************ free vector ******************/    helps to forecast when convergence will be reached. Elapsed time
 void free_vector(double*v, int nl, int nh)    is stamped in powell.  We created a new html file for the graphs
 {    concerning matrix of covariance. It has extension -cov.htm.
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 /************************ivector *******************************/    mle=-1 a template is output in file "or"mypar.txt with the design
 int *ivector(long nl,long nh)    of the covariance matrix to be input.
 {  
   int *v;    Revision 1.89  2003/06/24 12:30:52  brouard
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    (Module): Some bugs corrected for windows. Also, when
   if (!v) nrerror("allocation failure in ivector");    mle=-1 a template is output in file "or"mypar.txt with the design
   return v-nl+NR_END;    of the covariance matrix to be input.
 }  
     Revision 1.88  2003/06/23 17:54:56  brouard
 /******************free ivector **************************/    * 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.
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.87  2003/06/18 12:26:01  brouard
   free((FREE_ARG)(v+nl-NR_END));    Version 0.96
 }  
     Revision 1.86  2003/06/17 20:04:08  brouard
 /******************* imatrix *******************************/    (Module): Change position of html and gnuplot routines and added
 int **imatrix(long nrl, long nrh, long ncl, long nch)    routine fileappend.
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    Revision 1.85  2003/06/17 13:12:43  brouard
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    * 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
      prior to the death. In this case, dh was negative and likelihood
   /* allocate pointers to rows */    was wrong (infinity). We still send an "Error" but patch by
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    assuming that the date of death was just one stepm after the
   if (!m) nrerror("allocation failure 1 in matrix()");    interview.
   m += NR_END;    (Repository): Because some people have very long ID (first column)
   m -= nrl;    we changed int to long in num[] and we added a new lvector for
      memory allocation. But we also truncated to 8 characters (left
      truncation)
   /* allocate rows and set pointers to them */    (Repository): No more line truncation errors.
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.84  2003/06/13 21:44:43  brouard
   m[nrl] += NR_END;    * imach.c (Repository): Replace "freqsummary" at a correct
   m[nrl] -= ncl;    place. It differs from routine "prevalence" which may be called
      many times. Probs is memory consuming and must be used with
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    parcimony.
      Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.83  2003/06/10 13:39:11  lievre
 }    *** empty log message ***
   
 /****************** free_imatrix *************************/    Revision 1.82  2003/06/05 15:57:20  brouard
 void free_imatrix(m,nrl,nrh,ncl,nch)    Add log in  imach.c and  fullversion number is now printed.
       int **m;  
       long nch,ncl,nrh,nrl;  */
      /* free an int matrix allocated by imatrix() */  /*
 {     Interpolated Markov Chain
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Short summary of the programme:
 }    
     This program computes Healthy Life Expectancies from
 /******************* matrix *******************************/    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 double **matrix(long nrl, long nrh, long ncl, long nch)    first survey ("cross") where individuals from different ages are
 {    interviewed on their health status or degree of disability (in the
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    case of a health survey which is our main interest) -2- at least a
   double **m;    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    computed from the time spent in each health state according to a
   if (!m) nrerror("allocation failure 1 in matrix()");    model. More health states you consider, more time is necessary to reach the
   m += NR_END;    Maximum Likelihood of the parameters involved in the model.  The
   m -= nrl;    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    conditional to be observed in state i at the first wave. Therefore
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   m[nrl] += NR_END;    'age' is age and 'sex' is a covariate. If you want to have a more
   m[nrl] -= ncl;    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    you to do it.  More covariates you add, slower the
   return m;    convergence.
 }  
     The advantage of this computer programme, compared to a simple
 /*************************free matrix ************************/    multinomial logistic model, is clear when the delay between waves is not
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    identical for each individual. Also, if a individual missed an
 {    intermediate interview, the information is lost, but taken into
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    account using an interpolation or extrapolation.  
   free((FREE_ARG)(m+nrl-NR_END));  
 }    hPijx is the probability to be observed in state i at age x+h
     conditional to the observed state i at age x. The delay 'h' can be
 /******************* ma3x *******************************/    split into an exact number (nh*stepm) of unobserved intermediate
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    states. This elementary transition (by month, quarter,
 {    semester or year) is modelled as a multinomial logistic.  The hPx
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    matrix is simply the matrix product of nh*stepm elementary matrices
   double ***m;    and the contribution of each individual to the likelihood is simply
     hPijx.
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Also this programme outputs the covariance matrix of the parameters but also
   m += NR_END;    of the life expectancies. It also computes the period (stable) prevalence. 
   m -= nrl;    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));             Institut national d'études démographiques, Paris.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    This software have been partly granted by Euro-REVES, a concerted action
   m[nrl] += NR_END;    from the European Union.
   m[nrl] -= ncl;    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    can be accessed at http://euroreves.ined.fr/imach .
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   m[nrl][ncl] += NR_END;    
   m[nrl][ncl] -= nll;    **********************************************************************/
   for (j=ncl+1; j<=nch; j++)  /*
     m[nrl][j]=m[nrl][j-1]+nlay;    main
      read parameterfile
   for (i=nrl+1; i<=nrh; i++) {    read datafile
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    concatwav
     for (j=ncl+1; j<=nch; j++)    freqsummary
       m[i][j]=m[i][j-1]+nlay;    if (mle >= 1)
   }      mlikeli
   return m;    print results files
 }    if mle==1 
        computes hessian
 /*************************free ma3x ************************/    read end of parameter file: agemin, agemax, bage, fage, estepm
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)        begin-prev-date,...
 {    open gnuplot file
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    open html file
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
   free((FREE_ARG)(m+nrl-NR_END));     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
 }                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
       freexexit2 possible for memory heap.
 /***************** f1dim *************************/  
 extern int ncom;    h Pij x                         | pij_nom  ficrestpij
 extern double *pcom,*xicom;     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
 extern double (*nrfunc)(double []);         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
 double f1dim(double x)  
 {         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   int j;         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   double f;    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   double *xt;     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
       Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    forecasting if prevfcast==1 prevforecast call prevalence()
   f=(*nrfunc)(xt);    health expectancies
   free_vector(xt,1,ncom);    Variance-covariance of DFLE
   return f;    prevalence()
 }     movingaverage()
     varevsij() 
 /*****************brent *************************/    if popbased==1 varevsij(,popbased)
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    total life expectancies
 {    Variance of period (stable) prevalence
   int iter;   end
   double a,b,d,etemp;  */
   double fu,fv,fw,fx;  
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;   
    #include <math.h>
   a=(ax < cx ? ax : cx);  #include <stdio.h>
   b=(ax > cx ? ax : cx);  #include <stdlib.h>
   x=w=v=bx;  #include <string.h>
   fw=fv=fx=(*f)(x);  #include <unistd.h>
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  #include <limits.h>
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #include <sys/types.h>
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #include <sys/stat.h>
     printf(".");fflush(stdout);  #include <errno.h>
 #ifdef DEBUG  extern int errno;
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #ifdef LINUX
 #endif  #include <time.h>
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #include "timeval.h"
       *xmin=x;  #else
       return fx;  #include <sys/time.h>
     }  #endif
     ftemp=fu;  
     if (fabs(e) > tol1) {  #ifdef GSL
       r=(x-w)*(fx-fv);  #include <gsl/gsl_errno.h>
       q=(x-v)*(fx-fw);  #include <gsl/gsl_multimin.h>
       p=(x-v)*q-(x-w)*r;  #endif
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  /* #include <libintl.h> */
       q=fabs(q);  /* #define _(String) gettext (String) */
       etemp=e;  
       e=d;  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       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));  #define GNUPLOTPROGRAM "gnuplot"
       else {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
         d=p/q;  #define FILENAMELENGTH 132
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
           d=SIGN(tol1,xm-x);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       }  
     } else {  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #define NINTERVMAX 8
     fu=(*f)(u);  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
     if (fu <= fx) {  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
       if (u >= x) a=x; else b=x;  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
       SHFT(v,w,x,u)  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
         SHFT(fv,fw,fx,fu)  #define MAXN 20000
         } else {  #define YEARM 12. /**< Number of months per year */
           if (u < x) a=u; else b=u;  #define AGESUP 130
           if (fu <= fw || w == x) {  #define AGEBASE 40
             v=w;  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
             w=u;  #ifdef UNIX
             fv=fw;  #define DIRSEPARATOR '/'
             fw=fu;  #define CHARSEPARATOR "/"
           } else if (fu <= fv || v == x || v == w) {  #define ODIRSEPARATOR '\\'
             v=u;  #else
             fv=fu;  #define DIRSEPARATOR '\\'
           }  #define CHARSEPARATOR "\\"
         }  #define ODIRSEPARATOR '/'
   }  #endif
   nrerror("Too many iterations in brent");  
   *xmin=x;  /* $Id$ */
   return fx;  /* $State$ */
 }  
   char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
 /****************** mnbrak ***********************/  char fullversion[]="$Revision$ $Date$"; 
   char strstart[80];
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
             double (*func)(double))  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 {  int nvar=0, nforce=0; /* Number of variables, number of forces */
   double ulim,u,r,q, dum;  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   double fu;  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
    int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   *fa=(*func)(*ax);  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
   *fb=(*func)(*bx);  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   if (*fb > *fa) {  int cptcovprodnoage=0; /**< Number of covariate products without age */   
     SHFT(dum,*ax,*bx,dum)  int cptcoveff=0; /* Total number of covariates to vary for printing results */
       SHFT(dum,*fb,*fa,dum)  int cptcov=0; /* Working variable */
       }  int npar=NPARMAX;
   *cx=(*bx)+GOLD*(*bx-*ax);  int nlstate=2; /* Number of live states */
   *fc=(*func)(*cx);  int ndeath=1; /* Number of dead states */
   while (*fb > *fc) {  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     r=(*bx-*ax)*(*fb-*fc);  int popbased=0;
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  int *wav; /* Number of waves for this individuual 0 is possible */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  int maxwav=0; /* Maxim number of waves */
     ulim=(*bx)+GLIMIT*(*cx-*bx);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     if ((*bx-u)*(u-*cx) > 0.0) {  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       fu=(*func)(u);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     } else if ((*cx-u)*(u-ulim) > 0.0) {                     to the likelihood and the sum of weights (done by funcone)*/
       fu=(*func)(u);  int mle=1, weightopt=0;
       if (fu < *fc) {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
           SHFT(*fb,*fc,fu,(*func)(u))  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
           }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  double jmean=1; /* Mean space between 2 waves */
       u=ulim;  double **matprod2(); /* test */
       fu=(*func)(u);  double **oldm, **newm, **savm; /* Working pointers to matrices */
     } else {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       u=(*cx)+GOLD*(*cx-*bx);  /*FILE *fic ; */ /* Used in readdata only */
       fu=(*func)(u);  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     }  FILE *ficlog, *ficrespow;
     SHFT(*ax,*bx,*cx,u)  int globpr=0; /* Global variable for printing or not */
       SHFT(*fa,*fb,*fc,fu)  double fretone; /* Only one call to likelihood */
       }  long ipmx=0; /* Number of contributions */
 }  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
 /*************** linmin ************************/  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   FILE *ficresilk;
 int ncom;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 double *pcom,*xicom;  FILE *ficresprobmorprev;
 double (*nrfunc)(double []);  FILE *fichtm, *fichtmcov; /* Html File */
    FILE *ficreseij;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  char filerese[FILENAMELENGTH];
 {  FILE *ficresstdeij;
   double brent(double ax, double bx, double cx,  char fileresstde[FILENAMELENGTH];
                double (*f)(double), double tol, double *xmin);  FILE *ficrescveij;
   double f1dim(double x);  char filerescve[FILENAMELENGTH];
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  FILE  *ficresvij;
               double *fc, double (*func)(double));  char fileresv[FILENAMELENGTH];
   int j;  FILE  *ficresvpl;
   double xx,xmin,bx,ax;  char fileresvpl[FILENAMELENGTH];
   double fx,fb,fa;  char title[MAXLINE];
    char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   ncom=n;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   pcom=vector(1,n);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   xicom=vector(1,n);  char command[FILENAMELENGTH];
   nrfunc=func;  int  outcmd=0;
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     xicom[j]=xi[j];  
   }  char filelog[FILENAMELENGTH]; /* Log file */
   ax=0.0;  char filerest[FILENAMELENGTH];
   xx=1.0;  char fileregp[FILENAMELENGTH];
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  char popfile[FILENAMELENGTH];
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   for (j=1;j<=n;j++) {  struct timezone tzp;
     xi[j] *= xmin;  extern int gettimeofday();
     p[j] += xi[j];  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   }  long time_value;
   free_vector(xicom,1,n);  extern long time();
   free_vector(pcom,1,n);  char strcurr[80], strfor[80];
 }  
   char *endptr;
 /*************** powell ************************/  long lval;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  double dval;
             double (*func)(double []))  
 {  #define NR_END 1
   void linmin(double p[], double xi[], int n, double *fret,  #define FREE_ARG char*
               double (*func)(double []));  #define FTOL 1.0e-10
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  #define NRANSI 
   double fp,fptt;  #define ITMAX 200 
   double *xits;  
   pt=vector(1,n);  #define TOL 2.0e-4 
   ptt=vector(1,n);  
   xit=vector(1,n);  #define CGOLD 0.3819660 
   xits=vector(1,n);  #define ZEPS 1.0e-10 
   *fret=(*func)(p);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  #define GOLD 1.618034 
     fp=(*fret);  #define GLIMIT 100.0 
     ibig=0;  #define TINY 1.0e-20 
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  static double maxarg1,maxarg2;
     for (i=1;i<=n;i++)  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       printf(" %d %.12f",i, p[i]);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     printf("\n");    
     for (i=1;i<=n;i++) {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  #define rint(a) floor(a+0.5)
       fptt=(*fret);  
 #ifdef DEBUG  static double sqrarg;
       printf("fret=%lf \n",*fret);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #endif  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       printf("%d",i);fflush(stdout);  int agegomp= AGEGOMP;
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  int imx; 
         del=fabs(fptt-(*fret));  int stepm=1;
         ibig=i;  /* Stepm, step in month: minimum step interpolation*/
       }  
 #ifdef DEBUG  int estepm;
       printf("%d %.12e",i,(*fret));  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  int m,nb;
         printf(" x(%d)=%.12e",j,xit[j]);  long *num;
       }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       for(j=1;j<=n;j++)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
         printf(" p=%.12e",p[j]);  double **pmmij, ***probs;
       printf("\n");  double *ageexmed,*agecens;
 #endif  double dateintmean=0;
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  double *weight;
 #ifdef DEBUG  int **s; /* Status */
       int k[2],l;  double *agedc;
       k[0]=1;  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
       k[1]=-1;                    * covar=matrix(0,NCOVMAX,1,n); 
       printf("Max: %.12e",(*func)(p));                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       for (j=1;j<=n;j++)  double  idx; 
         printf(" %.12e",p[j]);  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
       printf("\n");  int *Ndum; /** Freq of modality (tricode */
       for(l=0;l<=1;l++) {  int **codtab; /**< codtab=imatrix(1,100,1,10); */
         for (j=1;j<=n;j++) {  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  double *lsurv, *lpop, *tpop;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  double ftolhess; /**< Tolerance for computing hessian */
       }  
 #endif  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
       free_vector(xit,1,n);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       free_vector(xits,1,n);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       free_vector(ptt,1,n);    */ 
       free_vector(pt,1,n);    char  *ss;                            /* pointer */
       return;    int   l1, l2;                         /* length counters */
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    l1 = strlen(path );                   /* length of path */
     for (j=1;j<=n;j++) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       ptt[j]=2.0*p[j]-pt[j];    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       xit[j]=p[j]-pt[j];    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       pt[j]=p[j];      strcpy( name, path );               /* we got the fullname name because no directory */
     }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     fptt=(*func)(ptt);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     if (fptt < fp) {      /* get current working directory */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      /*    extern  char* getcwd ( char *buf , int len);*/
       if (t < 0.0) {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         linmin(p,xit,n,fret,func);        return( GLOCK_ERROR_GETCWD );
         for (j=1;j<=n;j++) {      }
           xi[j][ibig]=xi[j][n];      /* got dirc from getcwd*/
           xi[j][n]=xit[j];      printf(" DIRC = %s \n",dirc);
         }    } else {                              /* strip direcotry from path */
 #ifdef DEBUG      ss++;                               /* after this, the filename */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      l2 = strlen( ss );                  /* length of filename */
         for(j=1;j<=n;j++)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
           printf(" %.12e",xit[j]);      strcpy( name, ss );         /* save file name */
         printf("\n");      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 #endif      dirc[l1-l2] = 0;                    /* add zero */
       }      printf(" DIRC2 = %s \n",dirc);
     }    }
   }    /* We add a separator at the end of dirc if not exists */
 }    l1 = strlen( dirc );                  /* length of directory */
     if( dirc[l1-1] != DIRSEPARATOR ){
 /**** Prevalence limit ****************/      dirc[l1] =  DIRSEPARATOR;
       dirc[l1+1] = 0; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      printf(" DIRC3 = %s \n",dirc);
 {    }
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    ss = strrchr( name, '.' );            /* find last / */
      matrix by transitions matrix until convergence is reached */    if (ss >0){
       ss++;
   int i, ii,j,k;      strcpy(ext,ss);                     /* save extension */
   double min, max, maxmin, maxmax,sumnew=0.;      l1= strlen( name);
   double **matprod2();      l2= strlen(ss)+1;
   double **out, cov[NCOVMAX], **pmij();      strncpy( finame, name, l1-l2);
   double **newm;      finame[l1-l2]= 0;
   double agefin, delaymax=50 ; /* Max number of years to converge */    }
   
   for (ii=1;ii<=nlstate+ndeath;ii++)    return( 0 );                          /* we're done */
     for (j=1;j<=nlstate+ndeath;j++){  }
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
     }  
   /******************************************/
    cov[1]=1.;  
    void replace_back_to_slash(char *s, char*t)
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  {
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    int i;
     newm=savm;    int lg=0;
     /* Covariates have to be included here again */    i=0;
      cov[2]=agefin;    lg=strlen(t);
      for(i=0; i<= lg; i++) {
       for (k=1; k<=cptcovn;k++) {      (s[i] = t[i]);
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      if (t[i]== '\\') s[i]='/';
         /*      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]]);*/    }
       }  }
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  char *trimbb(char *out, char *in)
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     char *s;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    s=out;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    while (*in != '\0'){
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        in++;
       }
     savm=oldm;      *out++ = *in++;
     oldm=newm;    }
     maxmax=0.;    *out='\0';
     for(j=1;j<=nlstate;j++){    return s;
       min=1.;  }
       max=0.;  
       for(i=1; i<=nlstate; i++) {  char *cutl(char *blocc, char *alocc, char *in, char occ)
         sumnew=0;  {
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
         prlim[i][j]= newm[i][j]/(1-sumnew);       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
         max=FMAX(max,prlim[i][j]);       gives blocc="abcdef2ghi" and alocc="j".
         min=FMIN(min,prlim[i][j]);       If occ is not found blocc is null and alocc is equal to in. Returns blocc
       }    */
       maxmin=max-min;    char *s, *t, *bl;
       maxmax=FMAX(maxmax,maxmin);    t=in;s=in;
     }    while ((*in != occ) && (*in != '\0')){
     if(maxmax < ftolpl){      *alocc++ = *in++;
       return prlim;    }
     }    if( *in == occ){
   }      *(alocc)='\0';
 }      s=++in;
     }
 /*************** transition probabilities ***************/   
     if (s == t) {/* occ not found */
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      *(alocc-(in-s))='\0';
 {      in=s;
   double s1, s2;    }
   /*double t34;*/    while ( *in != '\0'){
   int i,j,j1, nc, ii, jj;      *blocc++ = *in++;
     }
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){    *blocc='\0';
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    return t;
         /*s2 += param[i][j][nc]*cov[nc];*/  }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  char *cutv(char *blocc, char *alocc, char *in, char occ)
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  {
       }    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
       ps[i][j]=s2;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/       gives blocc="abcdef2ghi" and alocc="j".
     }       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     for(j=i+1; j<=nlstate+ndeath;j++){    */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    char *s, *t;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    t=in;s=in;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    while (*in != '\0'){
       }      while( *in == occ){
       ps[i][j]=s2;        *blocc++ = *in++;
     }        s=in;
   }      }
     /*ps[3][2]=1;*/      *blocc++ = *in++;
     }
   for(i=1; i<= nlstate; i++){    if (s == t) /* occ not found */
      s1=0;      *(blocc-(in-s))='\0';
     for(j=1; j<i; j++)    else
       s1+=exp(ps[i][j]);      *(blocc-(in-s)-1)='\0';
     for(j=i+1; j<=nlstate+ndeath; j++)    in=s;
       s1+=exp(ps[i][j]);    while ( *in != '\0'){
     ps[i][i]=1./(s1+1.);      *alocc++ = *in++;
     for(j=1; j<i; j++)    }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)    *alocc='\0';
       ps[i][j]= exp(ps[i][j])*ps[i][i];    return s;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  }
   } /* end i */  
   int nbocc(char *s, char occ)
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  {
     for(jj=1; jj<= nlstate+ndeath; jj++){    int i,j=0;
       ps[ii][jj]=0;    int lg=20;
       ps[ii][ii]=1;    i=0;
     }    lg=strlen(s);
   }    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
     }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    return j;
     for(jj=1; jj<= nlstate+ndeath; jj++){  }
      printf("%lf ",ps[ii][jj]);  
    }  /* void cutv(char *u,char *v, char*t, char occ) */
     printf("\n ");  /* { */
     }  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
     printf("\n ");printf("%lf ",cov[2]);*/  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
 /*  /*      gives u="abcdef2ghi" and v="j" *\/ */
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  /*   int i,lg,j,p=0; */
   goto end;*/  /*   i=0; */
     return ps;  /*   lg=strlen(t); */
 }  /*   for(j=0; j<=lg-1; j++) { */
   /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
 /**************** Product of 2 matrices ******************/  /*   } */
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  /*   for(j=0; j<p; j++) { */
 {  /*     (u[j] = t[j]); */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  /*   } */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  /*      u[p]='\0'; */
   /* in, b, out are matrice of pointers which should have been initialized  
      before: only the contents of out is modified. The function returns  /*    for(j=0; j<= lg; j++) { */
      a pointer to pointers identical to out */  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   long i, j, k;  /*   } */
   for(i=nrl; i<= nrh; i++)  /* } */
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  /********************** nrerror ********************/
         out[i][k] +=in[i][j]*b[j][k];  
   void nrerror(char error_text[])
   return out;  {
 }    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
 /************* Higher Matrix Product ***************/  }
   /*********************** vector *******************/
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  double *vector(int nl, int nh)
 {  {
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    double *v;
      duration (i.e. until    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    if (!v) nrerror("allocation failure in vector");
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    return v-nl+NR_END;
      (typically every 2 years instead of every month which is too big).  }
      Model is determined by parameters x and covariates have to be  
      included manually here.  /************************ free vector ******************/
   void free_vector(double*v, int nl, int nh)
      */  {
     free((FREE_ARG)(v+nl-NR_END));
   int i, j, d, h, k;  }
   double **out, cov[NCOVMAX];  
   double **newm;  /************************ivector *******************************/
   int *ivector(long nl,long nh)
   /* Hstepm could be zero and should return the unit matrix */  {
   for (i=1;i<=nlstate+ndeath;i++)    int *v;
     for (j=1;j<=nlstate+ndeath;j++){    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       oldm[i][j]=(i==j ? 1.0 : 0.0);    if (!v) nrerror("allocation failure in ivector");
       po[i][j][0]=(i==j ? 1.0 : 0.0);    return v-nl+NR_END;
     }  }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){  /******************free ivector **************************/
     for(d=1; d <=hstepm; d++){  void free_ivector(int *v, long nl, long nh)
       newm=savm;  {
       /* Covariates have to be included here again */    free((FREE_ARG)(v+nl-NR_END));
       cov[1]=1.;  }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /************************lvector *******************************/
       for (k=1; k<=cptcovage;k++)  long *lvector(long nl,long nh)
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  {
       for (k=1; k<=cptcovprod;k++)    long *v;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     if (!v) nrerror("allocation failure in ivector");
     return 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]);*/  
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  /******************free lvector **************************/
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  void free_lvector(long *v, long nl, long nh)
       savm=oldm;  {
       oldm=newm;    free((FREE_ARG)(v+nl-NR_END));
     }  }
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {  /******************* imatrix *******************************/
         po[i][j][h]=newm[i][j];  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
          */  { 
       }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   } /* end h */    int **m; 
   return po;    
 }    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
 /*************** log-likelihood *************/    m += NR_END; 
 double func( double *x)    m -= nrl; 
 {    
   int i, ii, j, k, mi, d, kk;    
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    /* allocate rows and set pointers to them */ 
   double **out;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   double sw; /* Sum of weights */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   double lli; /* Individual log likelihood */    m[nrl] += NR_END; 
   long ipmx;    m[nrl] -= ncl; 
   /*extern weight */    
   /* We are differentiating ll according to initial status */    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    
   /*for(i=1;i<imx;i++)    /* return pointer to array of pointers to rows */ 
     printf(" %d\n",s[4][i]);    return m; 
   */  } 
   cov[1]=1.;  
   /****************** free_imatrix *************************/
   for(k=1; k<=nlstate; k++) ll[k]=0.;  void free_imatrix(m,nrl,nrh,ncl,nch)
   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];        long nch,ncl,nrh,nrl; 
     for(mi=1; mi<= wav[i]-1; mi++){       /* free an int matrix allocated by imatrix() */ 
       for (ii=1;ii<=nlstate+ndeath;ii++)  { 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       for(d=0; d<dh[mi][i]; d++){    free((FREE_ARG) (m+nrl-NR_END)); 
         newm=savm;  } 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {  /******************* matrix *******************************/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  double **matrix(long nrl, long nrh, long ncl, long nch)
         }  {
            long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    double **m;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
         savm=oldm;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         oldm=newm;    if (!m) nrerror("allocation failure 1 in matrix()");
            m += NR_END;
            m -= nrl;
       } /* end mult */  
          m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    m[nrl] += NR_END;
       ipmx +=1;    m[nrl] -= ncl;
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     } /* end of wave */    return m;
   } /* end of individual */    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
   /* 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;  
 }  /*************************free matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
 /*********** Maximum Likelihood Estimation ***************/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  }
 {  
   int i,j, iter;  /******************* ma3x *******************************/
   double **xi,*delti;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   double fret;  {
   xi=matrix(1,npar,1,npar);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   for (i=1;i<=npar;i++)    double ***m;
     for (j=1;j<=npar;j++)  
       xi[i][j]=(i==j ? 1.0 : 0.0);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   printf("Powell\n");    if (!m) nrerror("allocation failure 1 in matrix()");
   powell(p,xi,npar,ftol,&iter,&fret,func);    m += NR_END;
     m -= nrl;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 }    m[nrl] += NR_END;
     m[nrl] -= ncl;
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 {  
   double  **a,**y,*x,pd;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   double **hess;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   int i, j,jk;    m[nrl][ncl] += NR_END;
   int *indx;    m[nrl][ncl] -= nll;
     for (j=ncl+1; j<=nch; j++) 
   double hessii(double p[], double delta, int theta, double delti[]);      m[nrl][j]=m[nrl][j-1]+nlay;
   double hessij(double p[], double delti[], int i, int j);    
   void lubksb(double **a, int npar, int *indx, double b[]) ;    for (i=nrl+1; i<=nrh; i++) {
   void ludcmp(double **a, int npar, int *indx, double *d) ;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (j=ncl+1; j<=nch; j++) 
   hess=matrix(1,npar,1,npar);        m[i][j]=m[i][j-1]+nlay;
     }
   printf("\nCalculation of the hessian matrix. Wait...\n");    return m; 
   for (i=1;i<=npar;i++){    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     printf("%d",i);fflush(stdout);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     hess[i][i]=hessii(p,ftolhess,i,delti);    */
     /*printf(" %f ",p[i]);*/  }
     /*printf(" %lf ",hess[i][i]);*/  
   }  /*************************free ma3x ************************/
    void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   for (i=1;i<=npar;i++) {  {
     for (j=1;j<=npar;j++)  {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       if (j>i) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         printf(".%d%d",i,j);fflush(stdout);    free((FREE_ARG)(m+nrl-NR_END));
         hess[i][j]=hessij(p,delti,i,j);  }
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/  /*************** function subdirf ***********/
       }  char *subdirf(char fileres[])
     }  {
   }    /* Caution optionfilefiname is hidden */
   printf("\n");    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    strcat(tmpout,fileres);
      return tmpout;
   a=matrix(1,npar,1,npar);  }
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);  /*************** function subdirf2 ***********/
   indx=ivector(1,npar);  char *subdirf2(char fileres[], char *preop)
   for (i=1;i<=npar;i++)  {
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    
   ludcmp(a,npar,indx,&pd);    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   for (j=1;j<=npar;j++) {    strcat(tmpout,"/");
     for (i=1;i<=npar;i++) x[i]=0;    strcat(tmpout,preop);
     x[j]=1;    strcat(tmpout,fileres);
     lubksb(a,npar,indx,x);    return tmpout;
     for (i=1;i<=npar;i++){  }
       matcov[i][j]=x[i];  
     }  /*************** function subdirf3 ***********/
   }  char *subdirf3(char fileres[], char *preop, char *preop2)
   {
   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,"/");
     }    strcat(tmpout,preop);
     printf("\n");    strcat(tmpout,preop2);
   }    strcat(tmpout,fileres);
     return tmpout;
   /* Recompute Inverse */  }
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  /***************** f1dim *************************/
   ludcmp(a,npar,indx,&pd);  extern int ncom; 
   extern double *pcom,*xicom;
   /*  printf("\n#Hessian matrix recomputed#\n");  extern double (*nrfunc)(double []); 
    
   for (j=1;j<=npar;j++) {  double f1dim(double x) 
     for (i=1;i<=npar;i++) x[i]=0;  { 
     x[j]=1;    int j; 
     lubksb(a,npar,indx,x);    double f;
     for (i=1;i<=npar;i++){    double *xt; 
       y[i][j]=x[i];   
       printf("%.3e ",y[i][j]);    xt=vector(1,ncom); 
     }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     printf("\n");    f=(*nrfunc)(xt); 
   }    free_vector(xt,1,ncom); 
   */    return f; 
   } 
   free_matrix(a,1,npar,1,npar);  
   free_matrix(y,1,npar,1,npar);  /*****************brent *************************/
   free_vector(x,1,npar);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   free_ivector(indx,1,npar);  { 
   free_matrix(hess,1,npar,1,npar);    int iter; 
     double a,b,d,etemp;
     double fu,fv,fw,fx;
 }    double ftemp;
     double p,q,r,tol1,tol2,u,v,w,x,xm; 
 /*************** hessian matrix ****************/    double e=0.0; 
 double hessii( double x[], double delta, int theta, double delti[])   
 {    a=(ax < cx ? ax : cx); 
   int i;    b=(ax > cx ? ax : cx); 
   int l=1, lmax=20;    x=w=v=bx; 
   double k1,k2;    fw=fv=fx=(*f)(x); 
   double p2[NPARMAX+1];    for (iter=1;iter<=ITMAX;iter++) { 
   double res;      xm=0.5*(a+b); 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   double fx;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   int k=0,kmax=10;      printf(".");fflush(stdout);
   double l1;      fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUG
   fx=func(x);      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);
   for (i=1;i<=npar;i++) p2[i]=x[i];      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   for(l=0 ; l <=lmax; l++){      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     l1=pow(10,l);  #endif
     delts=delt;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     for(k=1 ; k <kmax; k=k+1){        *xmin=x; 
       delt = delta*(l1*k);        return fx; 
       p2[theta]=x[theta] +delt;      } 
       k1=func(p2)-fx;      ftemp=fu;
       p2[theta]=x[theta]-delt;      if (fabs(e) > tol1) { 
       k2=func(p2)-fx;        r=(x-w)*(fx-fv); 
       /*res= (k1-2.0*fx+k2)/delt/delt; */        q=(x-v)*(fx-fw); 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        p=(x-v)*q-(x-w)*r; 
              q=2.0*(q-r); 
 #ifdef DEBUG        if (q > 0.0) p = -p; 
       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);        q=fabs(q); 
 #endif        etemp=e; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        e=d; 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         k=kmax;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       }        else { 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          d=p/q; 
         k=kmax; l=lmax*10.;          u=x+d; 
       }          if (u-a < tol2 || b-u < tol2) 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){            d=SIGN(tol1,xm-x); 
         delts=delt;        } 
       }      } else { 
     }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   }      } 
   delti[theta]=delts;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   return res;      fu=(*f)(u); 
        if (fu <= fx) { 
 }        if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
 double hessij( double x[], double delti[], int thetai,int thetaj)          SHFT(fv,fw,fx,fu) 
 {          } else { 
   int i;            if (u < x) a=u; else b=u; 
   int l=1, l1, lmax=20;            if (fu <= fw || w == x) { 
   double k1,k2,k3,k4,res,fx;              v=w; 
   double p2[NPARMAX+1];              w=u; 
   int k;              fv=fw; 
               fw=fu; 
   fx=func(x);            } else if (fu <= fv || v == x || v == w) { 
   for (k=1; k<=2; k++) {              v=u; 
     for (i=1;i<=npar;i++) p2[i]=x[i];              fv=fu; 
     p2[thetai]=x[thetai]+delti[thetai]/k;            } 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          } 
     k1=func(p2)-fx;    } 
      nrerror("Too many iterations in brent"); 
     p2[thetai]=x[thetai]+delti[thetai]/k;    *xmin=x; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    return fx; 
     k2=func(p2)-fx;  } 
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  /****************** mnbrak ***********************/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
                double (*func)(double)) 
     p2[thetai]=x[thetai]-delti[thetai]/k;  { 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    double ulim,u,r,q, dum;
     k4=func(p2)-fx;    double fu; 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */   
 #ifdef DEBUG    *fa=(*func)(*ax); 
     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);    *fb=(*func)(*bx); 
 #endif    if (*fb > *fa) { 
   }      SHFT(dum,*ax,*bx,dum) 
   return res;        SHFT(dum,*fb,*fa,dum) 
 }        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
 /************** Inverse of matrix **************/    *fc=(*func)(*cx); 
 void ludcmp(double **a, int n, int *indx, double *d)    while (*fb > *fc) { 
 {      r=(*bx-*ax)*(*fb-*fc); 
   int i,imax,j,k;      q=(*bx-*cx)*(*fb-*fa); 
   double big,dum,sum,temp;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   double *vv;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
        ulim=(*bx)+GLIMIT*(*cx-*bx); 
   vv=vector(1,n);      if ((*bx-u)*(u-*cx) > 0.0) { 
   *d=1.0;        fu=(*func)(u); 
   for (i=1;i<=n;i++) {      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     big=0.0;        fu=(*func)(u); 
     for (j=1;j<=n;j++)        if (fu < *fc) { 
       if ((temp=fabs(a[i][j])) > big) big=temp;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");            SHFT(*fb,*fc,fu,(*func)(u)) 
     vv[i]=1.0/big;            } 
   }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   for (j=1;j<=n;j++) {        u=ulim; 
     for (i=1;i<j;i++) {        fu=(*func)(u); 
       sum=a[i][j];      } else { 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        u=(*cx)+GOLD*(*cx-*bx); 
       a[i][j]=sum;        fu=(*func)(u); 
     }      } 
     big=0.0;      SHFT(*ax,*bx,*cx,u) 
     for (i=j;i<=n;i++) {        SHFT(*fa,*fb,*fc,fu) 
       sum=a[i][j];        } 
       for (k=1;k<j;k++)  } 
         sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  /*************** linmin ************************/
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;  int ncom; 
         imax=i;  double *pcom,*xicom;
       }  double (*nrfunc)(double []); 
     }   
     if (j != imax) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       for (k=1;k<=n;k++) {  { 
         dum=a[imax][k];    double brent(double ax, double bx, double cx, 
         a[imax][k]=a[j][k];                 double (*f)(double), double tol, double *xmin); 
         a[j][k]=dum;    double f1dim(double x); 
       }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       *d = -(*d);                double *fc, double (*func)(double)); 
       vv[imax]=vv[j];    int j; 
     }    double xx,xmin,bx,ax; 
     indx[j]=imax;    double fx,fb,fa;
     if (a[j][j] == 0.0) a[j][j]=TINY;   
     if (j != n) {    ncom=n; 
       dum=1.0/(a[j][j]);    pcom=vector(1,n); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    xicom=vector(1,n); 
     }    nrfunc=func; 
   }    for (j=1;j<=n;j++) { 
   free_vector(vv,1,n);  /* Doesn't work */      pcom[j]=p[j]; 
 ;      xicom[j]=xi[j]; 
 }    } 
     ax=0.0; 
 void lubksb(double **a, int n, int *indx, double b[])    xx=1.0; 
 {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   int i,ii=0,ip,j;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   double sum;  #ifdef DEBUG
      printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for (i=1;i<=n;i++) {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     ip=indx[i];  #endif
     sum=b[ip];    for (j=1;j<=n;j++) { 
     b[ip]=b[i];      xi[j] *= xmin; 
     if (ii)      p[j] += xi[j]; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    } 
     else if (sum) ii=i;    free_vector(xicom,1,n); 
     b[i]=sum;    free_vector(pcom,1,n); 
   }  } 
   for (i=n;i>=1;i--) {  
     sum=b[i];  char *asc_diff_time(long time_sec, char ascdiff[])
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  {
     b[i]=sum/a[i][i];    long sec_left, days, hours, minutes;
   }    days = (time_sec) / (60*60*24);
 }    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
 /************ Frequencies ********************/    sec_left = (sec_left) %(60*60);
 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)    minutes = (sec_left) /60;
 {  /* Some frequencies */    sec_left = (sec_left) % (60);
      sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    return ascdiff;
   double ***freq; /* Frequencies */  }
   double *pp;  
   double pos, k2, dateintsum=0,k2cpt=0;  /*************** powell ************************/
   FILE *ficresp;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   char fileresp[FILENAMELENGTH];              double (*func)(double [])) 
    { 
   pp=vector(1,nlstate);    void linmin(double p[], double xi[], int n, double *fret, 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);                double (*func)(double [])); 
   strcpy(fileresp,"p");    int i,ibig,j; 
   strcat(fileresp,fileres);    double del,t,*pt,*ptt,*xit;
   if((ficresp=fopen(fileresp,"w"))==NULL) {    double fp,fptt;
     printf("Problem with prevalence resultfile: %s\n", fileresp);    double *xits;
     exit(0);    int niterf, itmp;
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    pt=vector(1,n); 
   j1=0;    ptt=vector(1,n); 
      xit=vector(1,n); 
   j=cptcoveff;    xits=vector(1,n); 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    *fret=(*func)(p); 
      for (j=1;j<=n;j++) pt[j]=p[j]; 
   for(k1=1; k1<=j;k1++){    for (*iter=1;;++(*iter)) { 
     for(i1=1; i1<=ncodemax[k1];i1++){      fp=(*fret); 
       j1++;      ibig=0; 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      del=0.0; 
         scanf("%d", i);*/      last_time=curr_time;
       for (i=-1; i<=nlstate+ndeath; i++)        (void) gettimeofday(&curr_time,&tzp);
         for (jk=-1; jk<=nlstate+ndeath; jk++)        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);
           for(m=agemin; m <= agemax+3; m++)      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
             freq[i][jk][m]=0;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
           for (i=1;i<=n;i++) {
       dateintsum=0;        printf(" %d %.12f",i, p[i]);
       k2cpt=0;        fprintf(ficlog," %d %.12lf",i, p[i]);
       for (i=1; i<=imx; i++) {        fprintf(ficrespow," %.12lf", p[i]);
         bool=1;      }
         if  (cptcovn>0) {      printf("\n");
           for (z1=1; z1<=cptcoveff; z1++)      fprintf(ficlog,"\n");
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      fprintf(ficrespow,"\n");fflush(ficrespow);
               bool=0;      if(*iter <=3){
         }        tm = *localtime(&curr_time.tv_sec);
         if (bool==1) {        strcpy(strcurr,asctime(&tm));
           for(m=firstpass; m<=lastpass; m++){  /*       asctime_r(&tm,strcurr); */
             k2=anint[m][i]+(mint[m][i]/12.);        forecast_time=curr_time; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        itmp = strlen(strcurr);
               if(agev[m][i]==0) agev[m][i]=agemax+1;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
               if(agev[m][i]==1) agev[m][i]=agemax+2;          strcurr[itmp-1]='\0';
               if (m<lastpass) {        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        for(niterf=10;niterf<=30;niterf+=10){
               }          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
                        tmf = *localtime(&forecast_time.tv_sec);
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  /*      asctime_r(&tmf,strfor); */
                 dateintsum=dateintsum+k2;          strcpy(strfor,asctime(&tmf));
                 k2cpt++;          itmp = strlen(strfor);
               }          if(strfor[itmp-1]=='\n')
             }          strfor[itmp-1]='\0';
           }          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
         }          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       }        }
              }
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       if  (cptcovn>0) {        fptt=(*fret); 
         fprintf(ficresp, "\n#********** Variable ");  #ifdef DEBUG
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        printf("fret=%lf \n",*fret);
         fprintf(ficresp, "**********\n#");        fprintf(ficlog,"fret=%lf \n",*fret);
       }  #endif
       for(i=1; i<=nlstate;i++)        printf("%d",i);fflush(stdout);
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        fprintf(ficlog,"%d",i);fflush(ficlog);
       fprintf(ficresp, "\n");        linmin(p,xit,n,fret,func); 
              if (fabs(fptt-(*fret)) > del) { 
       for(i=(int)agemin; i <= (int)agemax+3; i++){          del=fabs(fptt-(*fret)); 
         if(i==(int)agemax+3)          ibig=i; 
           printf("Total");        } 
         else  #ifdef DEBUG
           printf("Age %d", i);        printf("%d %.12e",i,(*fret));
         for(jk=1; jk <=nlstate ; jk++){        fprintf(ficlog,"%d %.12e",i,(*fret));
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for (j=1;j<=n;j++) {
             pp[jk] += freq[jk][m][i];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         }          printf(" x(%d)=%.12e",j,xit[j]);
         for(jk=1; jk <=nlstate ; jk++){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
           for(m=-1, pos=0; m <=0 ; m++)        }
             pos += freq[jk][m][i];        for(j=1;j<=n;j++) {
           if(pp[jk]>=1.e-10)          printf(" p=%.12e",p[j]);
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          fprintf(ficlog," p=%.12e",p[j]);
           else        }
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        printf("\n");
         }        fprintf(ficlog,"\n");
   #endif
         for(jk=1; jk <=nlstate ; jk++){      } 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
             pp[jk] += freq[jk][m][i];  #ifdef DEBUG
         }        int k[2],l;
         k[0]=1;
         for(jk=1,pos=0; jk <=nlstate ; jk++)        k[1]=-1;
           pos += pp[jk];        printf("Max: %.12e",(*func)(p));
         for(jk=1; jk <=nlstate ; jk++){        fprintf(ficlog,"Max: %.12e",(*func)(p));
           if(pos>=1.e-5)        for (j=1;j<=n;j++) {
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          printf(" %.12e",p[j]);
           else          fprintf(ficlog," %.12e",p[j]);
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        }
           if( i <= (int) agemax){        printf("\n");
             if(pos>=1.e-5){        fprintf(ficlog,"\n");
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        for(l=0;l<=1;l++) {
               probs[i][jk][j1]= pp[jk]/pos;          for (j=1;j<=n;j++) {
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
             else            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          }
           }          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)));
                }
         for(jk=-1; jk <=nlstate+ndeath; jk++)  #endif
           for(m=-1; m <=nlstate+ndeath; m++)  
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
         if(i <= (int) agemax)        free_vector(xit,1,n); 
           fprintf(ficresp,"\n");        free_vector(xits,1,n); 
         printf("\n");        free_vector(ptt,1,n); 
       }        free_vector(pt,1,n); 
     }        return; 
   }      } 
   dateintmean=dateintsum/k2cpt;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
        for (j=1;j<=n;j++) { 
   fclose(ficresp);        ptt[j]=2.0*p[j]-pt[j]; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        xit[j]=p[j]-pt[j]; 
   free_vector(pp,1,nlstate);        pt[j]=p[j]; 
        } 
   /* End of Freq */      fptt=(*func)(ptt); 
 }      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 /************ Prevalence ********************/        if (t < 0.0) { 
 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)          linmin(p,xit,n,fret,func); 
 {  /* Some frequencies */          for (j=1;j<=n;j++) { 
              xi[j][ibig]=xi[j][n]; 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            xi[j][n]=xit[j]; 
   double ***freq; /* Frequencies */          }
   double *pp;  #ifdef DEBUG
   double pos, k2;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   pp=vector(1,nlstate);          for(j=1;j<=n;j++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            printf(" %.12e",xit[j]);
              fprintf(ficlog," %.12e",xit[j]);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          }
   j1=0;          printf("\n");
            fprintf(ficlog,"\n");
   j=cptcoveff;  #endif
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        }
        } 
   for(k1=1; k1<=j;k1++){    } 
     for(i1=1; i1<=ncodemax[k1];i1++){  } 
       j1++;  
        /**** Prevalence limit (stable or period prevalence)  ****************/
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)    double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
           for(m=agemin; m <= agemax+3; m++)  {
             freq[i][jk][m]=0;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
             matrix by transitions matrix until convergence is reached */
       for (i=1; i<=imx; i++) {  
         bool=1;    int i, ii,j,k;
         if  (cptcovn>0) {    double min, max, maxmin, maxmax,sumnew=0.;
           for (z1=1; z1<=cptcoveff; z1++)    /* double **matprod2(); */ /* test */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double **out, cov[NCOVMAX+1], **pmij();
               bool=0;    double **newm;
         }    double agefin, delaymax=50 ; /* Max number of years to converge */
         if (bool==1) {  
           for(m=firstpass; m<=lastpass; m++){    for (ii=1;ii<=nlstate+ndeath;ii++)
             k2=anint[m][i]+(mint[m][i]/12.);      for (j=1;j<=nlstate+ndeath;j++){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               if(agev[m][i]==0) agev[m][i]=agemax+1;      }
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {     cov[1]=1.;
                 if (calagedate>0)   
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                 else    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      newm=savm;
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];      /* Covariates have to be included here again */
               }      cov[2]=agefin;
             }      
           }      for (k=1; k<=cptcovn;k++) {
         }        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       }        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
       for(i=(int)agemin; i <= (int)agemax+3; i++){      }
         for(jk=1; jk <=nlstate ; jk++){      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
             pp[jk] += freq[jk][m][i];      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
         }      
         for(jk=1; jk <=nlstate ; jk++){      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
           for(m=-1, pos=0; m <=0 ; m++)      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
             pos += freq[jk][m][i];      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         }      /* 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 *\/ */
         for(jk=1; jk <=nlstate ; jk++){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      
             pp[jk] += freq[jk][m][i];      savm=oldm;
         }      oldm=newm;
              maxmax=0.;
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      for(j=1;j<=nlstate;j++){
                min=1.;
         for(jk=1; jk <=nlstate ; jk++){            max=0.;
           if( i <= (int) agemax){        for(i=1; i<=nlstate; i++) {
             if(pos>=1.e-5){          sumnew=0;
               probs[i][jk][j1]= pp[jk]/pos;          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);*/
         }          max=FMAX(max,prlim[i][j]);
                  min=FMIN(min,prlim[i][j]);
       }        }
     }        maxmin=max-min;
   }        maxmax=FMAX(maxmax,maxmin);
       }
        if(maxmax < ftolpl){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        return prlim;
   free_vector(pp,1,nlstate);      }
      }
 }  /* End of Freq */  }
   
 /************* Waves Concatenation ***************/  /*************** transition probabilities ***************/ 
   
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {  {
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    /* According to parameters values stored in x and the covariate's values stored in cov,
      Death is a valid wave (if date is known).       computes the probability to be observed in state j being in state i by appying the
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i       model to the ncovmodel covariates (including constant and age).
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
      and mw[mi+1][i]. dh depends on stepm.       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
      */       ncth covariate in the global vector x is given by the formula:
        j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
   int i, mi, m;       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
      double sum=0., jmean=0.;*/       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
        Outputs ps[i][j] the probability to be observed in j being in j according to
   int j, k=0,jk, ju, jl;       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   double sum=0.;    */
   jmin=1e+5;    double s1, lnpijopii;
   jmax=-1;    /*double t34;*/
   jmean=0.;    int i,j,j1, nc, ii, jj;
   for(i=1; i<=imx; i++){  
     mi=0;      for(i=1; i<= nlstate; i++){
     m=firstpass;        for(j=1; j<i;j++){
     while(s[m][i] <= nlstate){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       if(s[m][i]>=1)            /*lnpijopii += param[i][j][nc]*cov[nc];*/
         mw[++mi][i]=m;            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
       if(m >=lastpass)  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         break;          }
       else          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         m++;  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     }/* end while */        }
     if (s[m][i] > nlstate){        for(j=i+1; j<=nlstate+ndeath;j++){
       mi++;     /* Death is another wave */          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       /* if(mi==0)  never been interviewed correctly before death */            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
          /* Only death is a correct wave */            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
       mw[mi][i]=m;  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
     }          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     wav[i]=mi;        }
     if(mi==0)      }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      
   }      for(i=1; i<= nlstate; i++){
         s1=0;
   for(i=1; i<=imx; i++){        for(j=1; j<i; j++){
     for(mi=1; mi<wav[i];mi++){          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       if (stepm <=0)          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         dh[mi][i]=1;        }
       else{        for(j=i+1; j<=nlstate+ndeath; j++){
         if (s[mw[mi+1][i]][i] > nlstate) {          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           if (agedc[i] < 2*AGESUP) {          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        }
           if(j==0) j=1;  /* Survives at least one month after exam */        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
           k=k+1;        ps[i][i]=1./(s1+1.);
           if (j >= jmax) jmax=j;        /* Computing other pijs */
           if (j <= jmin) jmin=j;        for(j=1; j<i; j++)
           sum=sum+j;          ps[i][j]= exp(ps[i][j])*ps[i][i];
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        for(j=i+1; j<=nlstate+ndeath; j++)
           }          ps[i][j]= exp(ps[i][j])*ps[i][i];
         }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         else{      } /* end i */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      
           k=k+1;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
           if (j >= jmax) jmax=j;        for(jj=1; jj<= nlstate+ndeath; jj++){
           else if (j <= jmin)jmin=j;          ps[ii][jj]=0;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          ps[ii][ii]=1;
           sum=sum+j;        }
         }      }
         jk= j/stepm;      
         jl= j -jk*stepm;      
         ju= j -(jk+1)*stepm;      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
         if(jl <= -ju)      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
           dh[mi][i]=jk;      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
         else      /*   } */
           dh[mi][i]=jk+1;      /*   printf("\n "); */
         if(dh[mi][i]==0)      /* } */
           dh[mi][i]=1; /* At least one step */      /* printf("\n ");printf("%lf ",cov[2]);*/
       }      /*
     }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   }        goto end;*/
   jmean=sum/k;      return ps;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  }
  }  
 /*********** Tricode ****************************/  /**************** Product of 2 matrices ******************/
 void tricode(int *Tvar, int **nbcode, int imx)  
 {  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   int Ndum[20],ij=1, k, j, i;  {
   int cptcode=0;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   cptcoveff=0;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
      /* in, b, out are matrice of pointers which should have been initialized 
   for (k=0; k<19; k++) Ndum[k]=0;       before: only the contents of out is modified. The function returns
   for (k=1; k<=7; k++) ncodemax[k]=0;       a pointer to pointers identical to out */
     int i, j, k;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    for(i=nrl; i<= nrh; i++)
     for (i=1; i<=imx; i++) {      for(k=ncolol; k<=ncoloh; k++){
       ij=(int)(covar[Tvar[j]][i]);        out[i][k]=0.;
       Ndum[ij]++;        for(j=ncl; j<=nch; j++)
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          out[i][k] +=in[i][j]*b[j][k];
       if (ij > cptcode) cptcode=ij;      }
     }    return out;
   }
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;  
     }  /************* Higher Matrix Product ***************/
     ij=1;  
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
     for (i=1; i<=ncodemax[j]; i++) {    /* Computes the transition matrix starting at age 'age' over 
       for (k=0; k<=19; k++) {       'nhstepm*hstepm*stepm' months (i.e. until
         if (Ndum[k] != 0) {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           nbcode[Tvar[j]][ij]=k;       nhstepm*hstepm matrices. 
                 Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
           ij++;       (typically every 2 years instead of every month which is too big 
         }       for the memory).
         if (ij > ncodemax[j]) break;       Model is determined by parameters x and covariates have to be 
       }         included manually here. 
     }  
   }         */
   
  for (k=0; k<19; k++) Ndum[k]=0;    int i, j, d, h, k;
     double **out, cov[NCOVMAX+1];
  for (i=1; i<=ncovmodel-2; i++) {    double **newm;
       ij=Tvar[i];  
       Ndum[ij]++;    /* Hstepm could be zero and should return the unit matrix */
     }    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
  ij=1;        oldm[i][j]=(i==j ? 1.0 : 0.0);
  for (i=1; i<=10; i++) {        po[i][j][0]=(i==j ? 1.0 : 0.0);
    if((Ndum[i]!=0) && (i<=ncovcol)){      }
      Tvaraff[ij]=i;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
      ij++;    for(h=1; h <=nhstepm; h++){
    }      for(d=1; d <=hstepm; d++){
  }        newm=savm;
          /* Covariates have to be included here again */
     cptcoveff=ij-1;        cov[1]=1.;
 }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) 
 /*********** Health Expectancies ****************/          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
 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 )          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
 {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  
   double age, agelim, hf;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   double ***p3mat,***varhe;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   double **dnewm,**doldm;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   double *xp;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   double **gp, **gm;        savm=oldm;
   double ***gradg, ***trgradg;        oldm=newm;
   int theta;      }
       for(i=1; i<=nlstate+ndeath; i++)
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);        for(j=1;j<=nlstate+ndeath;j++) {
   xp=vector(1,npar);          po[i][j][h]=newm[i][j];
   dnewm=matrix(1,nlstate*2,1,npar);          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   doldm=matrix(1,nlstate*2,1,nlstate*2);        }
        /*printf("h=%d ",h);*/
   fprintf(ficreseij,"# Health expectancies\n");    } /* end h */
   fprintf(ficreseij,"# Age");  /*     printf("\n H=%d \n",h); */
   for(i=1; i<=nlstate;i++)    return po;
     for(j=1; j<=nlstate;j++)  }
       fprintf(ficreseij," %1d-%1d (SE)",i,j);  
   fprintf(ficreseij,"\n");  
   /*************** log-likelihood *************/
   if(estepm < stepm){  double func( double *x)
     printf ("Problem %d lower than %d\n",estepm, stepm);  {
   }    int i, ii, j, k, mi, d, kk;
   else  hstepm=estepm;      double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   /* We compute the life expectancy from trapezoids spaced every estepm months    double **out;
    * This is mainly to measure the difference between two models: for example    double sw; /* Sum of weights */
    * if stepm=24 months pijx are given only every 2 years and by summing them    double lli; /* Individual log likelihood */
    * we are calculating an estimate of the Life Expectancy assuming a linear    int s1, s2;
    * progression inbetween and thus overestimating or underestimating according    double bbh, survp;
    * to the curvature of the survival function. If, for the same date, we    long ipmx;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    /*extern weight */
    * to compare the new estimate of Life expectancy with the same linear    /* We are differentiating ll according to initial status */
    * hypothesis. A more precise result, taking into account a more precise    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
    * curvature will be obtained if estepm is as small as stepm. */    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
   /* 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.    cov[1]=1.;
      nhstepm is the number of hstepm from age to agelim  
      nstepm is the number of stepm from age to agelin.    for(k=1; k<=nlstate; k++) ll[k]=0.;
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like estepm months */    if(mle==1){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      survival function given by stepm (the optimization length). Unfortunately it        /* Computes the values of the ncovmodel covariates of the model
      means that if the survival funtion is printed only each two years of age and if           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
      you sum them up and add 1 year (area under the trapezoids) you won't get the same           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
      results. So we changed our mind and took the option of the best precision.           to be observed in j being in i according to the model.
   */         */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
           cov[2+k]=covar[Tvar[k]][i];
   agelim=AGESUP;        }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
     /* nhstepm age range expressed in number of stepm */           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
     nstepm=(int) rint((agelim-age)*YEARM/stepm);           has been calculated etc */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */        for(mi=1; mi<= wav[i]-1; mi++){
     /* if (stepm >= YEARM) hstepm=1;*/          for (ii=1;ii<=nlstate+ndeath;ii++)
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            for (j=1;j<=nlstate+ndeath;j++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     gp=matrix(0,nhstepm,1,nlstate*2);            }
     gm=matrix(0,nhstepm,1,nlstate*2);          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            for (kk=1; kk<=cptcovage;kk++) {
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
              }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     /* Computing Variances of health expectancies */            oldm=newm;
           } /* end mult */
      for(theta=1; theta <=npar; theta++){        
       for(i=1; i<=npar; i++){          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          /* But now since version 0.9 we anticipate for bias at large stepm.
       }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);             * (in months) between two waves is not a multiple of stepm, we rounded to 
             * the nearest (and in case of equal distance, to the lowest) interval but now
       cptj=0;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       for(j=1; j<= nlstate; j++){           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         for(i=1; i<=nlstate; i++){           * probability in order to take into account the bias as a fraction of the way
           cptj=cptj+1;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){           * -stepm/2 to stepm/2 .
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;           * For stepm=1 the results are the same as for previous versions of Imach.
           }           * 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; 
       for(i=1; i<=npar; i++)          /* bias bh is positive if real duration
         xp[i] = x[i] - (i==theta ?delti[theta]:0);           * is higher than the multiple of stepm and negative otherwise.
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);             */
                /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       cptj=0;          if( s2 > nlstate){ 
       for(j=1; j<= nlstate; j++){            /* i.e. if s2 is a death state and if the date of death is known 
         for(i=1;i<=nlstate;i++){               then the contribution to the likelihood is the probability to 
           cptj=cptj+1;               die between last step unit time and current  step unit time, 
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){               which is also equal to probability to die before dh 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;               minus probability to die before dh-stepm . 
           }               In version up to 0.92 likelihood was computed
         }          as if date of death was unknown. Death was treated as any other
       }          health state: the date of the interview describes the actual state
       for(j=1; j<= nlstate*2; j++)          and not the date of a change in health state. The former idea was
         for(h=0; h<=nhstepm-1; h++){          to consider that at each interview the state was recorded
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          (healthy, disable or death) and IMaCh was corrected; but when we
         }          introduced the exact date of death then we should have modified
      }          the contribution of an exact death to the likelihood. This new
              contribution is smaller and very dependent of the step unit
 /* End theta */          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);          interview up to one month before death multiplied by the
           probability to die within a month. Thanks to Chris
      for(h=0; h<=nhstepm-1; h++)          Jackson for correcting this bug.  Former versions increased
       for(j=1; j<=nlstate*2;j++)          mortality artificially. The bad side is that we add another loop
         for(theta=1; theta <=npar; theta++)          which slows down the processing. The difference can be up to 10%
           trgradg[h][j][theta]=gradg[h][theta][j];          lower mortality.
                  */
             lli=log(out[s1][s2] - savm[s1][s2]);
      for(i=1;i<=nlstate*2;i++)  
       for(j=1;j<=nlstate*2;j++)  
         varhe[i][j][(int)age] =0.;          } else if  (s2==-2) {
             for (j=1,survp=0. ; j<=nlstate; j++) 
      printf("%d|",(int)age);fflush(stdout);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
      for(h=0;h<=nhstepm-1;h++){            /*survp += out[s1][j]; */
       for(k=0;k<=nhstepm-1;k++){            lli= log(survp);
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);          }
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);          
         for(i=1;i<=nlstate*2;i++)          else if  (s2==-4) { 
           for(j=1;j<=nlstate*2;j++)            for (j=3,survp=0. ; j<=nlstate; j++)  
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       }            lli= log(survp); 
     }          } 
   
                else if  (s2==-5) { 
     /* Computing expectancies */            for (j=1,survp=0. ; j<=2; j++)  
     for(i=1; i<=nlstate;i++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       for(j=1; j<=nlstate;j++)            lli= log(survp); 
         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((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]);*/            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             /*  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 */
         }          } 
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     fprintf(ficreseij,"%3.0f",age );          /*if(lli ==000.0)*/
     cptj=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); */
     for(i=1; i<=nlstate;i++)          ipmx +=1;
       for(j=1; j<=nlstate;j++){          sw += weight[i];
         cptj++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        } /* end of wave */
       }      } /* end of individual */
     fprintf(ficreseij,"\n");    }  else if(mle==2){
          for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     free_matrix(gm,0,nhstepm,1,nlstate*2);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     free_matrix(gp,0,nhstepm,1,nlstate*2);        for(mi=1; mi<= wav[i]-1; mi++){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);          for (ii=1;ii<=nlstate+ndeath;ii++)
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(xp,1,npar);            }
   free_matrix(dnewm,1,nlstate*2,1,npar);          for(d=0; d<=dh[mi][i]; d++){
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);            newm=savm;
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);            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];
 /************ Variance ******************/            }
 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)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* Variance of health expectancies */            savm=oldm;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            oldm=newm;
   double **newm;          } /* end mult */
   double **dnewm,**doldm;        
   int i, j, nhstepm, hstepm, h, nstepm ;          s1=s[mw[mi][i]][i];
   int k, cptcode;          s2=s[mw[mi+1][i]][i];
   double *xp;          bbh=(double)bh[mi][i]/(double)stepm; 
   double **gp, **gm;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   double ***gradg, ***trgradg;          ipmx +=1;
   double ***p3mat;          sw += weight[i];
   double age,agelim, hf;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int theta;        } /* end of wave */
       } /* end of individual */
   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");    }  else if(mle==3){  /* exponential inter-extrapolation */
   fprintf(ficresvij,"# Age");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for(i=1; i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for(j=1; j<=nlstate;j++)        for(mi=1; mi<= wav[i]-1; mi++){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          for (ii=1;ii<=nlstate+ndeath;ii++)
   fprintf(ficresvij,"\n");            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   xp=vector(1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   dnewm=matrix(1,nlstate,1,npar);            }
   doldm=matrix(1,nlstate,1,nlstate);          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
   if(estepm < stepm){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     printf ("Problem %d lower than %d\n",estepm, stepm);            for (kk=1; kk<=cptcovage;kk++) {
   }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   else  hstepm=estepm;              }
   /* For example we decided to compute the life expectancy with the smallest unit */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      nhstepm is the number of hstepm from age to agelim            savm=oldm;
      nstepm is the number of stepm from age to agelin.            oldm=newm;
      Look at hpijx to understand the reason of that which relies in memory size          } /* end mult */
      and note for a fixed period like k years */        
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          s1=s[mw[mi][i]][i];
      survival function given by stepm (the optimization length). Unfortunately it          s2=s[mw[mi+1][i]][i];
      means that if the survival funtion is printed only each two years of age and if          bbh=(double)bh[mi][i]/(double)stepm; 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          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 */
      results. So we changed our mind and took the option of the best precision.          ipmx +=1;
   */          sw += weight[i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   agelim = AGESUP;        } /* end of wave */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      } /* end of individual */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
     gp=matrix(0,nhstepm,1,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
     gm=matrix(0,nhstepm,1,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(theta=1; theta <=npar; theta++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1; i<=npar; i++){ /* Computes gradient */            }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for(d=0; d<dh[mi][i]; d++){
       }            newm=savm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if (popbased==1) {            }
         for(i=1; i<=nlstate;i++)          
           prlim[i][i]=probs[(int)age][i][ij];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
       for(j=1; j<= nlstate; j++){            oldm=newm;
         for(h=0; h<=nhstepm; h++){          } /* end mult */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
       }          if( s2 > nlstate){ 
                lli=log(out[s1][s2] - savm[s1][s2]);
       for(i=1; i<=npar; i++) /* Computes gradient */          }else{
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          ipmx +=1;
            sw += weight[i];
       if (popbased==1) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(i=1; i<=nlstate;i++)  /*      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]); */
           prlim[i][i]=probs[(int)age][i][ij];        } /* end of wave */
       }      } /* end of individual */
     }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for(j=1; j<= nlstate; j++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(h=0; h<=nhstepm; h++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          for (ii=1;ii<=nlstate+ndeath;ii++)
         }            for (j=1;j<=nlstate+ndeath;j++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<= nlstate; j++)            }
         for(h=0; h<=nhstepm; h++){          for(d=0; d<dh[mi][i]; d++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     } /* End theta */            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            }
           
     for(h=0; h<=nhstepm; h++)            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(theta=1; theta <=npar; theta++)            savm=oldm;
           trgradg[h][j][theta]=gradg[h][theta][j];            oldm=newm;
           } /* end mult */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        
     for(i=1;i<=nlstate;i++)          s1=s[mw[mi][i]][i];
       for(j=1;j<=nlstate;j++)          s2=s[mw[mi+1][i]][i];
         vareij[i][j][(int)age] =0.;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
     for(h=0;h<=nhstepm;h++){          sw += weight[i];
       for(k=0;k<=nhstepm;k++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          /*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]);*/
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        } /* end of wave */
         for(i=1;i<=nlstate;i++)      } /* end of individual */
           for(j=1;j<=nlstate;j++)    } /* End of if */
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    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;
     fprintf(ficresvij,"%.0f ",age );  }
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  /*************** log-likelihood *************/
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  double funcone( double *x)
       }  {
     fprintf(ficresvij,"\n");    /* Same as likeli but slower because of a lot of printf and if */
     free_matrix(gp,0,nhstepm,1,nlstate);    int i, ii, j, k, mi, d, kk;
     free_matrix(gm,0,nhstepm,1,nlstate);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    double **out;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    double lli; /* Individual log likelihood */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double llt;
   } /* End age */    int s1, s2;
      double bbh, survp;
   free_vector(xp,1,npar);    /*extern weight */
   free_matrix(doldm,1,nlstate,1,npar);    /* We are differentiating ll according to initial status */
   free_matrix(dnewm,1,nlstate,1,nlstate);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
 }      printf(" %d\n",s[4][i]);
     */
 /************ Variance of prevlim ******************/    cov[1]=1.;
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  
 {    for(k=1; k<=nlstate; k++) ll[k]=0.;
   /* Variance of prevalence limit */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double **newm;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double **dnewm,**doldm;      for(mi=1; mi<= wav[i]-1; mi++){
   int i, j, nhstepm, hstepm;        for (ii=1;ii<=nlstate+ndeath;ii++)
   int k, cptcode;          for (j=1;j<=nlstate+ndeath;j++){
   double *xp;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *gp, *gm;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **gradg, **trgradg;          }
   double age,agelim;        for(d=0; d<dh[mi][i]; d++){
   int theta;          newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");          for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficresvpl,"# Age");            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for(i=1; i<=nlstate;i++)          }
       fprintf(ficresvpl," %1d-%1d",i,i);          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   fprintf(ficresvpl,"\n");          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   xp=vector(1,npar);          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
   dnewm=matrix(1,nlstate,1,npar);          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
   doldm=matrix(1,nlstate,1,nlstate);          savm=oldm;
            oldm=newm;
   hstepm=1*YEARM; /* Every year of age */        } /* end mult */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        
   agelim = AGESUP;        s1=s[mw[mi][i]][i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        s2=s[mw[mi+1][i]][i];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        bbh=(double)bh[mi][i]/(double)stepm; 
     if (stepm >= YEARM) hstepm=1;        /* bias is positive if real duration
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */         * is higher than the multiple of stepm and negative otherwise.
     gradg=matrix(1,npar,1,nlstate);         */
     gp=vector(1,nlstate);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     gm=vector(1,nlstate);          lli=log(out[s1][s2] - savm[s1][s2]);
         } else if  (s2==-2) {
     for(theta=1; theta <=npar; theta++){          for (j=1,survp=0. ; j<=nlstate; j++) 
       for(i=1; i<=npar; i++){ /* Computes gradient */            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          lli= log(survp);
       }        }else if (mle==1){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for(i=1;i<=nlstate;i++)        } else if(mle==2){
         gp[i] = prlim[i][i];          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
            } else if(mle==3){  /* exponential inter-extrapolation */
       for(i=1; i<=npar; i++) /* Computes gradient */          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 */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          lli=log(out[s1][s2]); /* Original formula */
       for(i=1;i<=nlstate;i++)        } else{  /* mle=0 back to 1 */
         gm[i] = prlim[i][i];          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*lli=log(out[s1][s2]); */ /* Original formula */
       for(i=1;i<=nlstate;i++)        } /* End of if */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        ipmx +=1;
     } /* End theta */        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     trgradg =matrix(1,nlstate,1,npar);        /*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]); */
         if(globpr){
     for(j=1; j<=nlstate;j++)          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
       for(theta=1; theta <=npar; theta++)   %11.6f %11.6f %11.6f ", \
         trgradg[j][theta]=gradg[theta][j];                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                   2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     for(i=1;i<=nlstate;i++)          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       varpl[i][(int)age] =0.;            llt +=ll[k]*gipmx/gsw;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          }
     for(i=1;i<=nlstate;i++)          fprintf(ficresilk," %10.6f\n", -llt);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        }
       } /* end of wave */
     fprintf(ficresvpl,"%.0f ",age );    } /* end of individual */
     for(i=1; i<=nlstate;i++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     fprintf(ficresvpl,"\n");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     free_vector(gp,1,nlstate);    if(globpr==0){ /* First time we count the contributions and weights */
     free_vector(gm,1,nlstate);      gipmx=ipmx;
     free_matrix(gradg,1,npar,1,nlstate);      gsw=sw;
     free_matrix(trgradg,1,nlstate,1,npar);    }
   } /* End age */    return -l;
   }
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
 }  {
     /* This routine should help understanding what is done with 
 /************ Variance of one-step probabilities  ******************/       the selection of individuals/waves and
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)       to check the exact contribution to the likelihood.
 {       Plotting could be done.
   int i, j, i1, k1, j1, z1;     */
   int k=0,l, cptcode;    int k;
   double **dnewm,**doldm;  
   double *xp;    if(*globpri !=0){ /* Just counts and sums, no printings */
   double *gp, *gm;      strcpy(fileresilk,"ilk"); 
   double **gradg, **trgradg;      strcat(fileresilk,fileres);
   double age,agelim, cov[NCOVMAX];      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   int theta;        printf("Problem with resultfile: %s\n", fileresilk);
   char fileresprob[FILENAMELENGTH];        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   char fileresprobcov[FILENAMELENGTH];      }
   char fileresprobcor[FILENAMELENGTH];      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 ");
   strcpy(fileresprob,"prob");      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   strcat(fileresprob,fileres);      for(k=1; k<=nlstate; k++) 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     printf("Problem with resultfile: %s\n", fileresprob);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   }    }
   strcpy(fileresprobcov,"probcov");  
   strcat(fileresprobcov,fileres);    *fretone=(*funcone)(p);
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    if(*globpri !=0){
     printf("Problem with resultfile: %s\n", fileresprobcov);      fclose(ficresilk);
   }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   strcpy(fileresprobcor,"probcor");      fflush(fichtm); 
   strcat(fileresprobcor,fileres);    } 
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    return;
     printf("Problem with resultfile: %s\n", fileresprobcor);  }
   }  
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);  
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);  /*********** Maximum Likelihood Estimation ***************/
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);  
    void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");  {
   fprintf(ficresprob,"# Age");    int i,j, iter;
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    double **xi;
   fprintf(ficresprobcov,"# Age");    double fret;
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    double fretone; /* Only one call to likelihood */
   fprintf(ficresprobcov,"# Age");    /*  char filerespow[FILENAMELENGTH];*/
   for(i=1; i<=nlstate;i++)    xi=matrix(1,npar,1,npar);
     for(j=1; j<=(nlstate+ndeath);j++){    for (i=1;i<=npar;i++)
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      for (j=1;j<=npar;j++)
       fprintf(ficresprobcov," p%1d-%1d ",i,j);        xi[i][j]=(i==j ? 1.0 : 0.0);
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     }      strcpy(filerespow,"pow"); 
   fprintf(ficresprob,"\n");    strcat(filerespow,fileres);
   fprintf(ficresprobcov,"\n");    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   fprintf(ficresprobcor,"\n");      printf("Problem with resultfile: %s\n", filerespow);
   xp=vector(1,npar);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    }
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    fprintf(ficrespow,"# Powell\n# iter -2*LL");
      for (i=1;i<=nlstate;i++)
   cov[1]=1;      for(j=1;j<=nlstate+ndeath;j++)
   j=cptcoveff;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    fprintf(ficrespow,"\n");
   j1=0;  
   for(k1=1; k1<=1;k1++){    powell(p,xi,npar,ftol,&iter,&fret,func);
     for(i1=1; i1<=ncodemax[k1];i1++){  
     j1++;    free_matrix(xi,1,npar,1,npar);
     fclose(ficrespow);
     if  (cptcovn>0) {    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       fprintf(ficresprob, "\n#********** Variable ");    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       fprintf(ficresprobcov, "\n#********** Variable ");    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       fprintf(ficresprobcor, "\n#********** Variable ");  
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  }
       fprintf(ficresprob, "**********\n#");  
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  /**** Computes Hessian and covariance matrix ***/
       fprintf(ficresprobcov, "**********\n#");  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  {
       fprintf(ficresprobcor, "**********\n#");    double  **a,**y,*x,pd;
     }    double **hess;
        int i, j,jk;
       for (age=bage; age<=fage; age ++){    int *indx;
         cov[2]=age;  
         for (k=1; k<=cptcovn;k++) {    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    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[]) ;
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    void ludcmp(double **a, int npar, int *indx, double *d) ;
         for (k=1; k<=cptcovprod;k++)    double gompertz(double p[]);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    hess=matrix(1,npar,1,npar);
          
         gradg=matrix(1,npar,1,9);    printf("\nCalculation of the hessian matrix. Wait...\n");
         trgradg=matrix(1,9,1,npar);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    for (i=1;i<=npar;i++){
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      printf("%d",i);fflush(stdout);
          fprintf(ficlog,"%d",i);fflush(ficlog);
         for(theta=1; theta <=npar; theta++){     
           for(i=1; i<=npar; i++)       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
             xp[i] = x[i] + (i==theta ?delti[theta]:0);      
                /*  printf(" %f ",p[i]);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
              }
           k=0;    
           for(i=1; i<= (nlstate+ndeath); i++){    for (i=1;i<=npar;i++) {
             for(j=1; j<=(nlstate+ndeath);j++){      for (j=1;j<=npar;j++)  {
               k=k+1;        if (j>i) { 
               gp[k]=pmmij[i][j];          printf(".%d%d",i,j);fflush(stdout);
             }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           }          hess[i][j]=hessij(p,delti,i,j,func,npar);
                    
           for(i=1; i<=npar; i++)          hess[j][i]=hess[i][j];    
             xp[i] = x[i] - (i==theta ?delti[theta]:0);          /*printf(" %lf ",hess[i][j]);*/
            }
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      }
           k=0;    }
           for(i=1; i<=(nlstate+ndeath); i++){    printf("\n");
             for(j=1; j<=(nlstate+ndeath);j++){    fprintf(ficlog,"\n");
               k=k+1;  
               gm[k]=pmmij[i][j];    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);
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    y=matrix(1,npar,1,npar);
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      x=vector(1,npar);
         }    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
           for(theta=1; theta <=npar; theta++)    ludcmp(a,npar,indx,&pd);
             trgradg[j][theta]=gradg[theta][j];  
            for (j=1;j<=npar;j++) {
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      for (i=1;i<=npar;i++) x[i]=0;
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      x[j]=1;
              lubksb(a,npar,indx,x);
         pmij(pmmij,cov,ncovmodel,x,nlstate);      for (i=1;i<=npar;i++){ 
                matcov[i][j]=x[i];
         k=0;      }
         for(i=1; i<=(nlstate+ndeath); i++){    }
           for(j=1; j<=(nlstate+ndeath);j++){  
             k=k+1;    printf("\n#Hessian matrix#\n");
             gm[k]=pmmij[i][j];    fprintf(ficlog,"\n#Hessian matrix#\n");
           }    for (i=1;i<=npar;i++) { 
         }      for (j=1;j<=npar;j++) { 
              printf("%.3e ",hess[i][j]);
         /*printf("\n%d ",(int)age);        fprintf(ficlog,"%.3e ",hess[i][j]);
      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]));      printf("\n");
      }*/      fprintf(ficlog,"\n");
     }
         fprintf(ficresprob,"\n%d ",(int)age);  
         fprintf(ficresprobcov,"\n%d ",(int)age);    /* Recompute Inverse */
         fprintf(ficresprobcor,"\n%d ",(int)age);    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    ludcmp(a,npar,indx,&pd);
           fprintf(ficresprob,"%12.3e (%12.3e) ",gm[i],sqrt(doldm[i][j]));  
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    /*  printf("\n#Hessian matrix recomputed#\n");
           fprintf(ficresprobcov,"%12.3e ",gm[i]);  
           fprintf(ficresprobcor,"%12.3e ",gm[i]);    for (j=1;j<=npar;j++) {
         }      for (i=1;i<=npar;i++) x[i]=0;
         i=0;      x[j]=1;
         for (k=1; k<=(nlstate);k++){      lubksb(a,npar,indx,x);
           for (l=1; l<=(nlstate+ndeath);l++){      for (i=1;i<=npar;i++){ 
             i=i++;        y[i][j]=x[i];
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);        printf("%.3e ",y[i][j]);
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);        fprintf(ficlog,"%.3e ",y[i][j]);
             for (j=1; j<=i;j++){      }
               fprintf(ficresprobcov," %12.3e",doldm[i][j]);      printf("\n");
               fprintf(ficresprobcor," %12.3e",doldm[i][j]/sqrt(doldm[i][i])/sqrt(doldm[j][j]));      fprintf(ficlog,"\n");
             }    }
           }    */
         }  
       }    free_matrix(a,1,npar,1,npar);
     }    free_matrix(y,1,npar,1,npar);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    free_vector(x,1,npar);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    free_ivector(indx,1,npar);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    free_matrix(hess,1,npar,1,npar);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
   }  
   free_vector(xp,1,npar);  }
   fclose(ficresprob);  
   fclose(ficresprobcov);  /*************** hessian matrix ****************/
   fclose(ficresprobcor);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 }  {
     int i;
     int l=1, lmax=20;
 /******************* Printing html file ***********/    double k1,k2;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    double p2[MAXPARM+1]; /* identical to x */
                   int lastpass, int stepm, int weightopt, char model[],\    double res;
                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\    double fx;
                   char version[], int popforecast, int estepm ,\    int k=0,kmax=10;
                   double jprev1, double mprev1,double anprev1, \    double l1;
                   double jprev2, double mprev2,double anprev2){  
   int jj1, k1, i1, cpt;    fx=func(x);
   FILE *fichtm;    for (i=1;i<=npar;i++) p2[i]=x[i];
   /*char optionfilehtm[FILENAMELENGTH];*/    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
       l1=pow(10,l);
   strcpy(optionfilehtm,optionfile);      delts=delt;
   strcat(optionfilehtm,".htm");      for(k=1 ; k <kmax; k=k+1){
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        delt = delta*(l1*k);
     printf("Problem with %s \n",optionfilehtm), exit(0);        p2[theta]=x[theta] +delt;
   }        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
         p2[theta]=x[theta]-delt;
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n        k2=func(p2)-fx;
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n        /*res= (k1-2.0*fx+k2)/delt/delt; */
 \n        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 Total number of observations=%d <br>\n        
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n  #ifdef DEBUGHESS
 <hr  size=\"2\" color=\"#EC5E5E\">        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);
  <ul><li>Parameter files<br>\n        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);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n  #endif
  - 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);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n          k=kmax;
  - 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        }
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n          k=kmax; l=lmax*10.;
  - Life expectancies by age and initial health status (estepm=%2d months):        }
    <a href=\"e%s\">e%s</a> <br>\n</li>", \        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);          delts=delt;
         }
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n      }
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    }
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    delti[theta]=delts;
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    return res; 
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n    
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n  }
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n  
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   {
  if(popforecast==1) fprintf(fichtm,"\n    int i;
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    int l=1, l1, lmax=20;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    double k1,k2,k3,k4,res,fx;
         <br>",fileres,fileres,fileres,fileres);    double p2[MAXPARM+1];
  else    int k;
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);  
 fprintf(fichtm," <li>Graphs</li><p>");    fx=func(x);
     for (k=1; k<=2; k++) {
  m=cptcoveff;      for (i=1;i<=npar;i++) p2[i]=x[i];
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
  jj1=0;      k1=func(p2)-fx;
  for(k1=1; k1<=m;k1++){    
    for(i1=1; i1<=ncodemax[k1];i1++){      p2[thetai]=x[thetai]+delti[thetai]/k;
      jj1++;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
      if (cptcovn > 0) {      k2=func(p2)-fx;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    
        for (cpt=1; cpt<=cptcoveff;cpt++)      p2[thetai]=x[thetai]-delti[thetai]/k;
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      k3=func(p2)-fx;
      }    
      /* Pij */      p2[thetai]=x[thetai]-delti[thetai]/k;
      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>      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          k4=func(p2)-fx;
      /* Quasi-incidences */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
      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>  #ifdef DEBUG
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      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);
        /* Stable prevalence in each health state */      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);
        for(cpt=1; cpt<nlstate;cpt++){  #endif
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    }
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    return res;
        }  }
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  /************** Inverse of matrix **************/
 interval) in state (%d): v%s%d%d.png <br>  void ludcmp(double **a, int n, int *indx, double *d) 
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    { 
      }    int i,imax,j,k; 
      for(cpt=1; cpt<=nlstate;cpt++) {    double big,dum,sum,temp; 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    double *vv; 
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);   
      }    vv=vector(1,n); 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    *d=1.0; 
 health expectancies in states (1) and (2): e%s%d.png<br>    for (i=1;i<=n;i++) { 
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      big=0.0; 
 fprintf(fichtm,"\n</body>");      for (j=1;j<=n;j++) 
    }        if ((temp=fabs(a[i][j])) > big) big=temp; 
  }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 fclose(fichtm);      vv[i]=1.0/big; 
 }    } 
     for (j=1;j<=n;j++) { 
 /******************* Gnuplot file **************/      for (i=1;i<j;i++) { 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        a[i][j]=sum; 
   int ng;      } 
   strcpy(optionfilegnuplot,optionfilefiname);      big=0.0; 
   strcat(optionfilegnuplot,".gp");      for (i=j;i<=n;i++) { 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        sum=a[i][j]; 
     printf("Problem with file %s",optionfilegnuplot);        for (k=1;k<j;k++) 
   }          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
 #ifdef windows        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     fprintf(ficgp,"cd \"%s\" \n",pathc);          big=dum; 
 #endif          imax=i; 
 m=pow(2,cptcoveff);        } 
        } 
  /* 1eme*/      if (j != imax) { 
   for (cpt=1; cpt<= nlstate ; cpt ++) {        for (k=1;k<=n;k++) { 
    for (k1=1; k1<= m ; k1 ++) {          dum=a[imax][k]; 
           a[imax][k]=a[j][k]; 
 #ifdef windows          a[j][k]=dum; 
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        } 
      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);        *d = -(*d); 
 #endif        vv[imax]=vv[j]; 
 #ifdef unix      } 
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      indx[j]=imax; 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      if (a[j][j] == 0.0) a[j][j]=TINY; 
 #endif      if (j != n) { 
         dum=1.0/(a[j][j]); 
 for (i=1; i<= nlstate ; i ++) {        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    } 
 }    free_vector(vv,1,n);  /* Doesn't work */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  ;
     for (i=1; i<= nlstate ; i ++) {  } 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  void lubksb(double **a, int n, int *indx, double b[]) 
 }  { 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    int i,ii=0,ip,j; 
      for (i=1; i<= nlstate ; i ++) {    double sum; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");   
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for (i=1;i<=n;i++) { 
 }        ip=indx[i]; 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      sum=b[ip]; 
 #ifdef unix      b[ip]=b[i]; 
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");      if (ii) 
 #endif        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
    }      else if (sum) ii=i; 
   }      b[i]=sum; 
   /*2 eme*/    } 
     for (i=n;i>=1;i--) { 
   for (k1=1; k1<= m ; k1 ++) {      sum=b[i]; 
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      b[i]=sum/a[i][i]; 
        } 
     for (i=1; i<= nlstate+1 ; i ++) {  } 
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  void pstamp(FILE *fichier)
       for (j=1; j<= nlstate+1 ; j ++) {  {
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  }
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  /************ Frequencies ********************/
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  {  /* Some frequencies */
       for (j=1; j<= nlstate+1 ; j ++) {    
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int i, m, jk, k1,i1, j1, bool, z1,j;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    int first;
 }      double ***freq; /* Frequencies */
       fprintf(ficgp,"\" t\"\" w l 0,");    double *pp, **prop;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       for (j=1; j<= nlstate+1 ; j ++) {    char fileresp[FILENAMELENGTH];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");    pp=vector(1,nlstate);
 }      prop=matrix(1,nlstate,iagemin,iagemax+3);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    strcpy(fileresp,"p");
       else fprintf(ficgp,"\" t\"\" w l 0,");    strcat(fileresp,fileres);
     }    if((ficresp=fopen(fileresp,"w"))==NULL) {
   }      printf("Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   /*3eme*/      exit(0);
     }
   for (k1=1; k1<= m ; k1 ++) {    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     for (cpt=1; cpt<= nlstate ; cpt ++) {    j1=0;
       k=2+nlstate*(2*cpt-2);    
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    j=cptcoveff;
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    first=1;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    /*    j1++;
   */
 */    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
       for (i=1; i< nlstate ; i ++) {        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         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);          scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
       }          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     }            for(m=iagemin; m <= iagemax+3; m++)
   }              freq[i][jk][m]=0;
          
   /* CV preval stat */        for (i=1; i<=nlstate; i++)  
     for (k1=1; k1<= m ; k1 ++) {          for(m=iagemin; m <= iagemax+3; m++)
     for (cpt=1; cpt<nlstate ; cpt ++) {            prop[i][m]=0;
       k=3;        
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        dateintsum=0;
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        k2cpt=0;
         for (i=1; i<=imx; i++) {
       for (i=1; i< nlstate ; i ++)          bool=1;
         fprintf(ficgp,"+$%d",k+i+1);          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            for (z1=1; z1<=cptcoveff; z1++)       
                    if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
       l=3+(nlstate+ndeath)*cpt;                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                bool=0;
       for (i=1; i< nlstate ; i ++) {                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
         l=3+(nlstate+ndeath)*cpt;                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
         fprintf(ficgp,"+$%d",l+i+1);                  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*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                } 
     }          }
   }     
            if (bool==1){
   /* proba elementaires */            for(m=firstpass; m<=lastpass; m++){
    for(i=1,jk=1; i <=nlstate; i++){              k2=anint[m][i]+(mint[m][i]/12.);
     for(k=1; k <=(nlstate+ndeath); k++){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       if (k != i) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         for(j=1; j <=ncovmodel; j++){                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];
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);                if (m<lastpass) {
           jk++;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           fprintf(ficgp,"\n");                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         }                }
       }                
     }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
    }                  dateintsum=dateintsum+k2;
                   k2cpt++;
    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 \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);            }
        if (ng==2)          }
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");        } /* end i */
        else         
          fprintf(ficgp,"\nset title \"Probability\"\n");        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        pstamp(ficresp);
        i=1;        if  (cptcovn>0) {
        for(k2=1; k2<=nlstate; k2++) {          fprintf(ficresp, "\n#********** Variable "); 
          k3=i;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
          for(k=1; k<=(nlstate+ndeath); k++) {          fprintf(ficresp, "**********\n#");
            if (k != k2){          fprintf(ficlog, "\n#********** Variable "); 
              if(ng==2)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);          fprintf(ficlog, "**********\n#");
              else        }
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        for(i=1; i<=nlstate;i++) 
              ij=1;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
              for(j=3; j <=ncovmodel; j++) {        fprintf(ficresp, "\n");
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        for(i=iagemin; i <= iagemax+3; i++){
                  ij++;          if(i==iagemax+3){
                }            fprintf(ficlog,"Total");
                else          }else{
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            if(first==1){
              }              first=0;
              fprintf(ficgp,")/(1");              printf("See log file for details...\n");
                          }
              for(k1=1; k1 <=nlstate; k1++){              fprintf(ficlog,"Age %d", i);
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          }
                ij=1;          for(jk=1; jk <=nlstate ; jk++){
                for(j=3; j <=ncovmodel; j++){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              pp[jk] += freq[jk][m][i]; 
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          }
                    ij++;          for(jk=1; jk <=nlstate ; jk++){
                  }            for(m=-1, pos=0; m <=0 ; m++)
                  else              pos += freq[jk][m][i];
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            if(pp[jk]>=1.e-10){
                }              if(first==1){
                fprintf(ficgp,")");                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
              }              }
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            }else{
              i=i+ncovmodel;              if(first==1)
            }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
          }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
        }            }
      }          }
    }  
    fclose(ficgp);          for(jk=1; jk <=nlstate ; jk++){
 }  /* end gnuplot */            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
           }       
 /*************** Moving average **************/          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){            pos += pp[jk];
             posprop += prop[jk][i];
   int i, cpt, cptcod;          }
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          for(jk=1; jk <=nlstate ; jk++){
       for (i=1; i<=nlstate;i++)            if(pos>=1.e-5){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)              if(first==1)
           mobaverage[(int)agedeb][i][cptcod]=0.;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                  fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){            }else{
       for (i=1; i<=nlstate;i++){              if(first==1)
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           for (cpt=0;cpt<=4;cpt++){              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];            }
           }            if( i <= iagemax){
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;              if(pos>=1.e-5){
         }                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]);*/
                  }
 }              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
 /************** Forecasting ******************/          }
 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(jk=-1; jk <=nlstate+ndeath; jk++)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            for(m=-1; m <=nlstate+ndeath; m++)
   int *popage;              if(freq[jk][m][i] !=0 ) {
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              if(first==1)
   double *popeffectif,*popcount;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   double ***p3mat;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   char fileresf[FILENAMELENGTH];              }
           if(i <= iagemax)
  agelim=AGESUP;            fprintf(ficresp,"\n");
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          if(first==1)
             printf("Others in log...\n");
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          fprintf(ficlog,"\n");
          }
          /*}*/
   strcpy(fileresf,"f");    }
   strcat(fileresf,fileres);    dateintmean=dateintsum/k2cpt; 
   if((ficresf=fopen(fileresf,"w"))==NULL) {   
     printf("Problem with forecast resultfile: %s\n", fileresf);    fclose(ficresp);
   }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    /* End of Freq */
   }
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /************ Prevalence ********************/
     movingaverage(agedeb, fage, ageminpar, mobaverage);  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)
   }  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   stepsize=(int) (stepm+YEARM-1)/YEARM;       in each health status at the date of interview (if between dateprev1 and dateprev2).
   if (stepm<=12) stepsize=1;       We still use firstpass and lastpass as another selection.
      */
   agelim=AGESUP;   
      int i, m, jk, k1, i1, j1, bool, z1,j;
   hstepm=1;    double ***freq; /* Frequencies */
   hstepm=hstepm/stepm;    double *pp, **prop;
   yp1=modf(dateintmean,&yp);    double pos,posprop; 
   anprojmean=yp;    double  y2; /* in fractional years */
   yp2=modf((yp1*12),&yp);    int iagemin, iagemax;
   mprojmean=yp;    int first; /** to stop verbosity which is redirected to log file */
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;    iagemin= (int) agemin;
   if(jprojmean==0) jprojmean=1;    iagemax= (int) agemax;
   if(mprojmean==0) jprojmean=1;    /*pp=vector(1,nlstate);*/
      prop=matrix(1,nlstate,iagemin,iagemax+3); 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
      j1=0;
   for(cptcov=1;cptcov<=i2;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    /*j=cptcoveff;*/
       k=k+1;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       fprintf(ficresf,"\n#******");    
       for(j=1;j<=cptcoveff;j++) {    first=1;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
       }      /*for(i1=1; i1<=ncodemax[k1];i1++){
       fprintf(ficresf,"******\n");        j1++;*/
       fprintf(ficresf,"# StartingAge FinalAge");        
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        for (i=1; i<=nlstate; i++)  
                for(m=iagemin; m <= iagemax+3; m++)
                  prop[i][m]=0.0;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {       
         fprintf(ficresf,"\n");        for (i=1; i<=imx; i++) { /* Each individual */
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            bool=1;
           if  (cptcovn>0) {
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            for (z1=1; z1<=cptcoveff; z1++) 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           nhstepm = nhstepm/hstepm;                bool=0;
                    } 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if (bool==1) { 
           oldm=oldms;savm=savms;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                      if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
           for (h=0; h<=nhstepm; h++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             if (h==(int) (calagedate+YEARM*cpt)) {                if(agev[m][i]==1) agev[m][i]=iagemax+2;
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
             }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
             for(j=1; j<=nlstate+ndeath;j++) {                  /*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]]);*/
               kk1=0.;kk2=0;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
               for(i=1; i<=nlstate;i++) {                                prop[s[m][i]][iagemax+3] += weight[i]; 
                 if (mobilav==1)                } 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];              }
                 else {            } /* end selection of waves */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          }
                 }        }
                        for(i=iagemin; i <= iagemax+3; i++){  
               }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
               if (h==(int)(calagedate+12*cpt)){            posprop += prop[jk][i]; 
                 fprintf(ficresf," %.3f", kk1);          } 
                                  
               }          for(jk=1; jk <=nlstate ; jk++){     
             }            if( i <=  iagemax){ 
           }              if(posprop>=1.e-5){ 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                probs[i][jk][j1]= prop[jk][i]/posprop;
         }              } else{
       }                if(first==1){
     }                  first=0;
   }                  printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
                        }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              }
             } 
   fclose(ficresf);          }/* end jk */ 
 }        }/* end i */ 
 /************** Forecasting ******************/      /*} *//* end i1 */
 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){    } /* end j1 */
      
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   int *popage;    /*free_vector(pp,1,nlstate);*/
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   double *popeffectif,*popcount;  }  /* End of prevalence */
   double ***p3mat,***tabpop,***tabpopprev;  
   char filerespop[FILENAMELENGTH];  /************* Waves Concatenation ***************/
   
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  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)
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  {
   agelim=AGESUP;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;       Death is a valid wave (if date is known).
         mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         and mw[mi+1][i]. dh depends on stepm.
         */
   strcpy(filerespop,"pop");  
   strcat(filerespop,fileres);    int i, mi, m;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     printf("Problem with forecast resultfile: %s\n", filerespop);       double sum=0., jmean=0.;*/
   }    int first;
   printf("Computing forecasting: result on file '%s' \n", filerespop);    int j, k=0,jk, ju, jl;
     double sum=0.;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    first=0;
     jmin=1e+5;
   if (mobilav==1) {    jmax=-1;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    jmean=0.;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    for(i=1; i<=imx; i++){
   }      mi=0;
       m=firstpass;
   stepsize=(int) (stepm+YEARM-1)/YEARM;      while(s[m][i] <= nlstate){
   if (stepm<=12) stepsize=1;        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
            mw[++mi][i]=m;
   agelim=AGESUP;        if(m >=lastpass)
            break;
   hstepm=1;        else
   hstepm=hstepm/stepm;          m++;
        }/* end while */
   if (popforecast==1) {      if (s[m][i] > nlstate){
     if((ficpop=fopen(popfile,"r"))==NULL) {        mi++;     /* Death is another wave */
       printf("Problem with population file : %s\n",popfile);exit(0);        /* if(mi==0)  never been interviewed correctly before death */
     }           /* Only death is a correct wave */
     popage=ivector(0,AGESUP);        mw[mi][i]=m;
     popeffectif=vector(0,AGESUP);      }
     popcount=vector(0,AGESUP);  
          wav[i]=mi;
     i=1;        if(mi==0){
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        nbwarn++;
            if(first==0){
     imx=i;          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          first=1;
   }        }
         if(first==1){
   for(cptcov=1;cptcov<=i2;cptcov++){          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        }
       k=k+1;      } /* end mi==0 */
       fprintf(ficrespop,"\n#******");    } /* End individuals */
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for(i=1; i<=imx; i++){
       }      for(mi=1; mi<wav[i];mi++){
       fprintf(ficrespop,"******\n");        if (stepm <=0)
       fprintf(ficrespop,"# Age");          dh[mi][i]=1;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);        else{
       if (popforecast==1)  fprintf(ficrespop," [Population]");          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                  if (agedc[i] < 2*AGESUP) {
       for (cpt=0; cpt<=0;cpt++) {              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                if(j==0) j=1;  /* Survives at least one month after exam */
                      else if(j<0){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){                nberr++;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                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]);
           nhstepm = nhstepm/hstepm;                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);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                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]);
           oldm=oldms;savm=savms;                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);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                }
                      k=k+1;
           for (h=0; h<=nhstepm; h++){              if (j >= jmax){
             if (h==(int) (calagedate+YEARM*cpt)) {                jmax=j;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                ijmax=i;
             }              }
             for(j=1; j<=nlstate+ndeath;j++) {              if (j <= jmin){
               kk1=0.;kk2=0;                jmin=j;
               for(i=1; i<=nlstate;i++) {                              ijmin=i;
                 if (mobilav==1)              }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];              sum=sum+j;
                 else {              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                 }            }
               }          }
               if (h==(int)(calagedate+12*cpt)){          else{
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
                   /*fprintf(ficrespop," %.3f", kk1);  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }            k=k+1;
             }            if (j >= jmax) {
             for(i=1; i<=nlstate;i++){              jmax=j;
               kk1=0.;              ijmax=i;
                 for(j=1; j<=nlstate;j++){            }
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];            else if (j <= jmin){
                 }              jmin=j;
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];              ijmin=i;
             }            }
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)            /*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]);*/
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);            if(j<0){
           }              nberr++;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              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]);
         }              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]);
       }            }
              sum=sum+j;
   /******/          }
           jk= j/stepm;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          jl= j -jk*stepm;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            ju= j -(jk+1)*stepm;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            if(jl==0){
           nhstepm = nhstepm/hstepm;              dh[mi][i]=jk;
                        bh[mi][i]=0;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }else{ /* We want a negative bias in order to only have interpolation ie
           oldm=oldms;savm=savms;                    * to avoid the price of an extra matrix product in likelihood */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                dh[mi][i]=jk+1;
           for (h=0; h<=nhstepm; h++){              bh[mi][i]=ju;
             if (h==(int) (calagedate+YEARM*cpt)) {            }
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          }else{
             }            if(jl <= -ju){
             for(j=1; j<=nlstate+ndeath;j++) {              dh[mi][i]=jk;
               kk1=0.;kk2=0;              bh[mi][i]=jl;       /* bias is positive if real duration
               for(i=1; i<=nlstate;i++) {                                                 * is higher than the multiple of stepm and negative otherwise.
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                                       */
               }            }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);            else{
             }              dh[mi][i]=jk+1;
           }              bh[mi][i]=ju;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
         }            if(dh[mi][i]==0){
       }              dh[mi][i]=1; /* At least one step */
    }              bh[mi][i]=ju; /* At least one step */
   }              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
              }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          } /* end if mle */
         }
   if (popforecast==1) {      } /* end wave */
     free_ivector(popage,0,AGESUP);    }
     free_vector(popeffectif,0,AGESUP);    jmean=sum/k;
     free_vector(popcount,0,AGESUP);    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
   }    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   }
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   fclose(ficrespop);  /*********** Tricode ****************************/
 }  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   {
 /***********************************************/    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
 /**************** Main Program *****************/    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
 /***********************************************/    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
      * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
 int main(int argc, char *argv[])    /* nbcode[Tvar[j]][1]= 
 {    */
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   double agedeb, agefin,hf;    int modmaxcovj=0; /* Modality max of covariates j */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    int cptcode=0; /* Modality max of covariates j */
     int modmincovj=0; /* Modality min of covariates j */
   double fret;  
   double **xi,tmp,delta;  
     cptcoveff=0; 
   double dum; /* Dummy variable */   
   double ***p3mat;    for (k=-1; k < maxncov; k++) Ndum[k]=0;
   int *indx;    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];    /* Loop on covariates without age and products */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
                                   modality of this covariate Vj*/ 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                                       * If product of Vn*Vm, still boolean *:
   char filerest[FILENAMELENGTH];                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
   char fileregp[FILENAMELENGTH];                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
   char popfile[FILENAMELENGTH];        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                                        modality of the nth covariate of individual i. */
   int firstobs=1, lastobs=10;        if (ij > modmaxcovj)
   int sdeb, sfin; /* Status at beginning and end */          modmaxcovj=ij; 
   int c,  h , cpt,l;        else if (ij < modmincovj) 
   int ju,jl, mi;          modmincovj=ij; 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        if ((ij < -1) && (ij > NCOVMAX)){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   int mobilav=0,popforecast=0;          exit(1);
   int hstepm, nhstepm;        }else
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   double bage, fage, age, agelim, agebase;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   double ftolpl=FTOL;        /* getting the maximum value of the modality of the covariate
   double **prlim;           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
   double *severity;           female is 1, then modmaxcovj=1.*/
   double ***param; /* Matrix of parameters */      }
   double  *p;      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   double **matcov; /* Matrix of covariance */      cptcode=modmaxcovj;
   double ***delti3; /* Scale */      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
   double *delti; /* Scale */     /*for (i=0; i<=cptcode; i++) {*/
   double ***eij, ***vareij;      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
   double **varpl; /* Variances of prevalence limits by age */        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
   double *epj, vepp;        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
   double kk1, kk2;          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        }
          /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
            historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
   char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";      } /* Ndum[-1] number of undefined modalities */
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
       /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
       /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
   char z[1]="c", occ;      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
 #include <sys/time.h>         modmincovj=3; modmaxcovj = 7;
 #include <time.h>         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];         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.
   /* long total_usecs;         nbcode[Tvar[j]][ij]=k;
   struct timeval start_time, end_time;         nbcode[Tvar[j]][1]=0;
           nbcode[Tvar[j]][2]=1;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */         nbcode[Tvar[j]][3]=2;
   getcwd(pathcd, size);      */
       ij=1; /* ij is similar to i but can jumps over null modalities */
   printf("\n%s",version);      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
   if(argc <=1){        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
     printf("\nEnter the parameter file name: ");          /*recode from 0 */
     scanf("%s",pathtot);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
   }            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
   else{                                       k is a modality. If we have model=V1+V1*sex 
     strcpy(pathtot,argv[1]);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   }            ij++;
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          }
   /*cygwin_split_path(pathtot,path,optionfile);          if (ij > ncodemax[j]) break; 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        }  /* end of loop on */
   /* cutv(path,optionfile,pathtot,'\\');*/      } /* end of loop on modality */ 
     } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
   chdir(path);    
   replace(pathc,path);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
      /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
 /*-------- arguments in the command line --------*/     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
      Ndum[ij]++; 
   strcpy(fileres,"r");   } 
   strcat(fileres, optionfilefiname);  
   strcat(fileres,".txt");    /* Other files have txt extension */   ij=1;
    for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   /*---------arguments file --------*/     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
      if((Ndum[i]!=0) && (i<=ncovcol)){
   if((ficpar=fopen(optionfile,"r"))==NULL)    {       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
     printf("Problem with optionfile %s\n",optionfile);       Tvaraff[ij]=i; /*For printing (unclear) */
     goto end;       ij++;
   }     }else
          Tvaraff[ij]=0;
   strcpy(filereso,"o");   }
   strcat(filereso,fileres);   ij--;
   if((ficparo=fopen(filereso,"w"))==NULL) {   cptcoveff=ij; /*Number of total covariates*/
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }  }
   
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  /*********** Health Expectancies ****************/
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
     puts(line);  
     fputs(line,ficparo);  {
   }    /* Health expectancies, no variances */
   ungetc(c,ficpar);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     int nhstepma, nstepma; /* Decreasing with age */
   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);    double age, agelim, hf;
   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);    double ***p3mat;
   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);    double eip;
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    pstamp(ficreseij);
     fgets(line, MAXLINE, ficpar);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     puts(line);    fprintf(ficreseij,"# Age");
     fputs(line,ficparo);    for(i=1; i<=nlstate;i++){
   }      for(j=1; j<=nlstate;j++){
   ungetc(c,ficpar);        fprintf(ficreseij," e%1d%1d ",i,j);
        }
          fprintf(ficreseij," e%1d. ",i);
   covar=matrix(0,NCOVMAX,1,n);    }
   cptcovn=0;    fprintf(ficreseij,"\n");
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
     
   ncovmodel=2+cptcovn;    if(estepm < stepm){
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
   /* Read guess parameters */    else  hstepm=estepm;   
   /* Reads comments: lines beginning with '#' */    /* We compute the life expectancy from trapezoids spaced every estepm months
   while((c=getc(ficpar))=='#' && c!= EOF){     * This is mainly to measure the difference between two models: for example
     ungetc(c,ficpar);     * if stepm=24 months pijx are given only every 2 years and by summing them
     fgets(line, MAXLINE, ficpar);     * we are calculating an estimate of the Life Expectancy assuming a linear 
     puts(line);     * progression in between and thus overestimating or underestimating according
     fputs(line,ficparo);     * 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
   ungetc(c,ficpar);     * to compare the new estimate of Life expectancy with the same linear 
       * hypothesis. A more precise result, taking into account a more precise
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);     * curvature will be obtained if estepm is as small as stepm. */
     for(i=1; i <=nlstate; i++)  
     for(j=1; j <=nlstate+ndeath-1; j++){    /* For example we decided to compute the life expectancy with the smallest unit */
       fscanf(ficpar,"%1d%1d",&i1,&j1);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       fprintf(ficparo,"%1d%1d",i1,j1);       nhstepm is the number of hstepm from age to agelim 
       printf("%1d%1d",i,j);       nstepm is the number of stepm from age to agelin. 
       for(k=1; k<=ncovmodel;k++){       Look at hpijx to understand the reason of that which relies in memory size
         fscanf(ficpar," %lf",&param[i][j][k]);       and note for a fixed period like estepm months */
         printf(" %lf",param[i][j][k]);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         fprintf(ficparo," %lf",param[i][j][k]);       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
       fscanf(ficpar,"\n");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       printf("\n");       results. So we changed our mind and took the option of the best precision.
       fprintf(ficparo,"\n");    */
     }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    agelim=AGESUP;
     /* If stepm=6 months */
   p=param[1][1];      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   /* Reads comments: lines beginning with '#' */      
   while((c=getc(ficpar))=='#' && c!= EOF){  /* nhstepm age range expressed in number of stepm */
     ungetc(c,ficpar);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     fgets(line, MAXLINE, ficpar);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     puts(line);    /* if (stepm >= YEARM) hstepm=1;*/
     fputs(line,ficparo);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   }    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   ungetc(c,ficpar);  
     for (age=bage; age<=fage; age ++){ 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   for(i=1; i <=nlstate; i++){      /* if (stepm >= YEARM) hstepm=1;*/
     for(j=1; j <=nlstate+ndeath-1; j++){      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);      /* If stepm=6 months */
       fprintf(ficparo,"%1d%1d",i1,j1);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
       for(k=1; k<=ncovmodel;k++){         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
         fscanf(ficpar,"%le",&delti3[i][j][k]);      
         printf(" %le",delti3[i][j][k]);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
         fprintf(ficparo," %le",delti3[i][j][k]);      
       }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       fscanf(ficpar,"\n");      
       printf("\n");      printf("%d|",(int)age);fflush(stdout);
       fprintf(ficparo,"\n");      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     }      
   }      /* Computing expectancies */
   delti=delti3[1][1];      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
   /* Reads comments: lines beginning with '#' */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   while((c=getc(ficpar))=='#' && c!= EOF){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     ungetc(c,ficpar);            
     fgets(line, MAXLINE, ficpar);            /* 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]);*/
     puts(line);  
     fputs(line,ficparo);          }
   }  
   ungetc(c,ficpar);      fprintf(ficreseij,"%3.0f",age );
        for(i=1; i<=nlstate;i++){
   matcov=matrix(1,npar,1,npar);        eip=0;
   for(i=1; i <=npar; i++){        for(j=1; j<=nlstate;j++){
     fscanf(ficpar,"%s",&str);          eip +=eij[i][j][(int)age];
     printf("%s",str);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
     fprintf(ficparo,"%s",str);        }
     for(j=1; j <=i; j++){        fprintf(ficreseij,"%9.4f", eip );
       fscanf(ficpar," %le",&matcov[i][j]);      }
       printf(" %.5le",matcov[i][j]);      fprintf(ficreseij,"\n");
       fprintf(ficparo," %.5le",matcov[i][j]);      
     }    }
     fscanf(ficpar,"\n");    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");    printf("\n");
     fprintf(ficparo,"\n");    fprintf(ficlog,"\n");
   }    
   for(i=1; i <=npar; i++)  }
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];  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[] )
      
   printf("\n");  {
     /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
     /*-------- Rewriting paramater file ----------*/    */
      strcpy(rfileres,"r");    /* "Rparameterfile */    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    int nhstepma, nstepma; /* Decreasing with age */
      strcat(rfileres,".");    /* */    double age, agelim, hf;
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    double ***p3matp, ***p3matm, ***varhe;
     if((ficres =fopen(rfileres,"w"))==NULL) {    double **dnewm,**doldm;
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    double *xp, *xm;
     }    double **gp, **gm;
     fprintf(ficres,"#%s\n",version);    double ***gradg, ***trgradg;
        int theta;
     /*-------- data file ----------*/  
     if((fic=fopen(datafile,"r"))==NULL)    {    double eip, vip;
       printf("Problem with datafile: %s\n", datafile);goto end;  
     }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
     n= lastobs;    xm=vector(1,npar);
     severity = vector(1,maxwav);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     outcome=imatrix(1,maxwav+1,1,n);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     num=ivector(1,n);    
     moisnais=vector(1,n);    pstamp(ficresstdeij);
     annais=vector(1,n);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     moisdc=vector(1,n);    fprintf(ficresstdeij,"# Age");
     andc=vector(1,n);    for(i=1; i<=nlstate;i++){
     agedc=vector(1,n);      for(j=1; j<=nlstate;j++)
     cod=ivector(1,n);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
     weight=vector(1,n);      fprintf(ficresstdeij," e%1d. ",i);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    }
     mint=matrix(1,maxwav,1,n);    fprintf(ficresstdeij,"\n");
     anint=matrix(1,maxwav,1,n);  
     s=imatrix(1,maxwav+1,1,n);    pstamp(ficrescveij);
     adl=imatrix(1,maxwav+1,1,n);        fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     tab=ivector(1,NCOVMAX);    fprintf(ficrescveij,"# Age");
     ncodemax=ivector(1,8);    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
     i=1;        cptj= (j-1)*nlstate+i;
     while (fgets(line, MAXLINE, fic) != NULL)    {        for(i2=1; i2<=nlstate;i2++)
       if ((i >= firstobs) && (i <=lastobs)) {          for(j2=1; j2<=nlstate;j2++){
                    cptj2= (j2-1)*nlstate+i2;
         for (j=maxwav;j>=1;j--){            if(cptj2 <= cptj)
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           strcpy(line,stra);          }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      }
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficrescveij,"\n");
         }    
            if(estepm < stepm){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      printf ("Problem %d lower than %d\n",estepm, stepm);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    }
     else  hstepm=estepm;   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    /* We compute the life expectancy from trapezoids spaced every estepm months
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);     * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);     * we are calculating an estimate of the Life Expectancy assuming a linear 
         for (j=ncovcol;j>=1;j--){     * progression in between and thus overestimating or underestimating according
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);     * 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
         num[i]=atol(stra);     * to compare the new estimate of Life expectancy with the same linear 
             * hypothesis. A more precise result, taking into account a more precise
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){     * curvature will be obtained if estepm is as small as stepm. */
           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;}*/  
     /* For example we decided to compute the life expectancy with the smallest unit */
         i=i+1;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       }       nhstepm is the number of hstepm from age to agelim 
     }       nstepm is the number of stepm from age to agelin. 
     /* printf("ii=%d", ij);       Look at hpijx to understand the reason of that which relies in memory size
        scanf("%d",i);*/       and note for a fixed period like estepm months */
   imx=i-1; /* Number of individuals */    /* 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
   /* for (i=1; i<=imx; i++){       means that if the survival funtion is printed only each two years of age and if
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;       results. So we changed our mind and took the option of the best precision.
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    */
     }*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    /*  for (i=1; i<=imx; i++){  
      if (s[4][i]==9)  s[4][i]=-1;    /* If stepm=6 months */
      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]));}*/    /* nhstepm age range expressed in number of stepm */
      agelim=AGESUP;
      nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
   /* Calculation of the number of parameter from char model*/    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   Tvar=ivector(1,15);    /* if (stepm >= YEARM) hstepm=1;*/
   Tprod=ivector(1,15);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   Tvaraff=ivector(1,15);    
   Tvard=imatrix(1,15,1,2);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   Tage=ivector(1,15);          p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   if (strlen(model) >1){    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     j=0, j1=0, k1=1, k2=1;    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     j=nbocc(model,'+');    gm=matrix(0,nhstepm,1,nlstate*nlstate);
     j1=nbocc(model,'*');  
     cptcovn=j+1;    for (age=bage; age<=fage; age ++){ 
     cptcovprod=j1;      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
          /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     strcpy(modelsav,model);      /* if (stepm >= YEARM) hstepm=1;*/
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       printf("Error. Non available option model=%s ",model);  
       goto end;      /* If stepm=6 months */
     }      /* Computed by stepm unit matrices, product of hstepma matrices, stored
             in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     for(i=(j+1); i>=1;i--){      
       cutv(stra,strb,modelsav,'+');      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      /* Computing  Variances of health expectancies */
       /*scanf("%d",i);*/      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
       if (strchr(strb,'*')) {         decrease memory allocation */
         cutv(strd,strc,strb,'*');      for(theta=1; theta <=npar; theta++){
         if (strcmp(strc,"age")==0) {        for(i=1; i<=npar; i++){ 
           cptcovprod--;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           cutv(strb,stre,strd,'V');          xm[i] = x[i] - (i==theta ?delti[theta]:0);
           Tvar[i]=atoi(stre);        }
           cptcovage++;        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
             Tage[cptcovage]=i;        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
             /*printf("stre=%s ", stre);*/    
         }        for(j=1; j<= nlstate; j++){
         else if (strcmp(strd,"age")==0) {          for(i=1; i<=nlstate; i++){
           cptcovprod--;            for(h=0; h<=nhstepm-1; h++){
           cutv(strb,stre,strc,'V');              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
           Tvar[i]=atoi(stre);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
           cptcovage++;            }
           Tage[cptcovage]=i;          }
         }        }
         else {       
           cutv(strb,stre,strc,'V');        for(ij=1; ij<= nlstate*nlstate; ij++)
           Tvar[i]=ncovcol+k1;          for(h=0; h<=nhstepm-1; h++){
           cutv(strb,strc,strd,'V');            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           Tprod[k1]=i;          }
           Tvard[k1][1]=atoi(strc);      }/* End theta */
           Tvard[k1][2]=atoi(stre);      
           Tvar[cptcovn+k2]=Tvard[k1][1];      
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      for(h=0; h<=nhstepm-1; h++)
           for (k=1; k<=lastobs;k++)        for(j=1; j<=nlstate*nlstate;j++)
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          for(theta=1; theta <=npar; theta++)
           k1++;            trgradg[h][j][theta]=gradg[h][theta][j];
           k2=k2+2;      
         }  
       }       for(ij=1;ij<=nlstate*nlstate;ij++)
       else {        for(ji=1;ji<=nlstate*nlstate;ji++)
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          varhe[ij][ji][(int)age] =0.;
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');       printf("%d|",(int)age);fflush(stdout);
       Tvar[i]=atoi(strc);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       }       for(h=0;h<=nhstepm-1;h++){
       strcpy(modelsav,stra);          for(k=0;k<=nhstepm-1;k++){
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         scanf("%d",i);*/          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++)
                varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);        }
   printf("cptcovprod=%d ", cptcovprod);      }
   scanf("%d ",i);*/  
     fclose(fic);      /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     /*  if(mle==1){*/      for(i=1; i<=nlstate;i++)
     if (weightopt != 1) { /* Maximisation without weights*/        for(j=1; j<=nlstate;j++)
       for(i=1;i<=n;i++) weight[i]=1.0;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     }            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
     /*-calculation of age at interview from date of interview and age at death -*/            
     agev=matrix(1,maxwav,1,imx);            /* 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 (i=1; i<=imx; i++) {          }
       for(m=2; (m<= maxwav); m++) {  
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      fprintf(ficresstdeij,"%3.0f",age );
          anint[m][i]=9999;      for(i=1; i<=nlstate;i++){
          s[m][i]=-1;        eip=0.;
        }        vip=0.;
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;        for(j=1; j<=nlstate;j++){
       }          eip += eij[i][j][(int)age];
     }          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
     for (i=1; i<=imx; i++)  {          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        }
       for(m=1; (m<= maxwav); m++){        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
         if(s[m][i] >0){      }
           if (s[m][i] >= nlstate+1) {      fprintf(ficresstdeij,"\n");
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)      fprintf(ficrescveij,"%3.0f",age );
                 agev[m][i]=agedc[i];      for(i=1; i<=nlstate;i++)
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/        for(j=1; j<=nlstate;j++){
            else {          cptj= (j-1)*nlstate+i;
               if (andc[i]!=9999){          for(i2=1; i2<=nlstate;i2++)
               printf("Warning negative age at death: %d line:%d\n",num[i],i);            for(j2=1; j2<=nlstate;j2++){
               agev[m][i]=-1;              cptj2= (j2-1)*nlstate+i2;
               }              if(cptj2 <= cptj)
             }                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
           }            }
           else if(s[m][i] !=9){ /* Should no more exist */        }
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      fprintf(ficrescveij,"\n");
             if(mint[m][i]==99 || anint[m][i]==9999)     
               agev[m][i]=1;    }
             else if(agev[m][i] <agemin){    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
               agemin=agev[m][i];    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
             }    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
             else if(agev[m][i] >agemax){    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               agemax=agev[m][i];    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    printf("\n");
             }    fprintf(ficlog,"\n");
             /*agev[m][i]=anint[m][i]-annais[i];*/  
             /*   agev[m][i] = age[i]+2*m;*/    free_vector(xm,1,npar);
           }    free_vector(xp,1,npar);
           else { /* =9 */    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
             agev[m][i]=1;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
             s[m][i]=-1;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
           }  }
         }  
         else /*= 0 Unknown */  /************ Variance ******************/
           agev[m][i]=1;  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);*/
     for (i=1; i<=imx; i++)  {    /* double **newm;*/
       for(m=1; (m<= maxwav); m++){    double **dnewm,**doldm;
         if (s[m][i] > (nlstate+ndeath)) {    double **dnewmp,**doldmp;
           printf("Error: Wrong value in nlstate or ndeath\n");      int i, j, nhstepm, hstepm, h, nstepm ;
           goto end;    int k, cptcode;
         }    double *xp;
       }    double **gp, **gm;  /* for var eij */
     }    double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     free_vector(severity,1,maxwav);    double ***p3mat;
     free_imatrix(outcome,1,maxwav+1,1,n);    double age,agelim, hf;
     free_vector(moisnais,1,n);    double ***mobaverage;
     free_vector(annais,1,n);    int theta;
     /* free_matrix(mint,1,maxwav,1,n);    char digit[4];
        free_matrix(anint,1,maxwav,1,n);*/    char digitp[25];
     free_vector(moisdc,1,n);  
     free_vector(andc,1,n);    char fileresprobmorprev[FILENAMELENGTH];
   
        if(popbased==1){
     wav=ivector(1,imx);      if(mobilav!=0)
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        strcpy(digitp,"-populbased-mobilav-");
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      else strcpy(digitp,"-populbased-nomobil-");
        }
     /* Concatenates waves */    else 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      strcpy(digitp,"-stablbased-");
   
     if (mobilav!=0) {
       Tcode=ivector(1,100);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       ncodemax[1]=1;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
            }
    codtab=imatrix(1,100,1,10);    }
    h=0;  
    m=pow(2,cptcoveff);    strcpy(fileresprobmorprev,"prmorprev"); 
      sprintf(digit,"%-d",ij);
    for(k=1;k<=cptcoveff; k++){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
      for(i=1; i <=(m/pow(2,k));i++){    strcat(fileresprobmorprev,digit); /* Tvar to be done */
        for(j=1; j <= ncodemax[k]; j++){    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    strcat(fileresprobmorprev,fileres);
            h++;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
          }    }
        }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      }   
    }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    pstamp(ficresprobmorprev);
       codtab[1][2]=1;codtab[2][2]=2; */    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);
    /* for(i=1; i <=m ;i++){    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       for(k=1; k <=cptcovn; k++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);      fprintf(ficresprobmorprev," p.%-d SE",j);
       }      for(i=1; i<=nlstate;i++)
       printf("\n");        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       }    }  
       scanf("%d",i);*/    fprintf(ficresprobmorprev,"\n");
        fprintf(ficgp,"\n# Routine varevsij");
    /* Calculates basic frequencies. Computes observed prevalence at single age    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
        and prints on file fileres'p'. */    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
      /*   } */
        varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pstamp(ficresvij);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if(popbased==1)
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      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);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    else
            fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     /* For Powell, parameters are in a vector p[] starting at p[1]    fprintf(ficresvij,"# Age");
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    for(i=1; i<=nlstate;i++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     if(mle==1){    fprintf(ficresvij,"\n");
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }    xp=vector(1,npar);
        dnewm=matrix(1,nlstate,1,npar);
     /*--------- results files --------------*/    doldm=matrix(1,nlstate,1,nlstate);
     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);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
      doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
    jk=1;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    gpp=vector(nlstate+1,nlstate+ndeath);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    gmp=vector(nlstate+1,nlstate+ndeath);
    for(i=1,jk=1; i <=nlstate; i++){    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      for(k=1; k <=(nlstate+ndeath); k++){    
        if (k != i)    if(estepm < stepm){
          {      printf ("Problem %d lower than %d\n",estepm, stepm);
            printf("%d%d ",i,k);    }
            fprintf(ficres,"%1d%1d ",i,k);    else  hstepm=estepm;   
            for(j=1; j <=ncovmodel; j++){    /* For example we decided to compute the life expectancy with the smallest unit */
              printf("%f ",p[jk]);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
              fprintf(ficres,"%f ",p[jk]);       nhstepm is the number of hstepm from age to agelim 
              jk++;       nstepm is the number of stepm from age to agelin. 
            }       Look at function hpijx to understand why (it is linked to memory size questions) */
            printf("\n");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
            fprintf(ficres,"\n");       survival function given by stepm (the optimization length). Unfortunately it
          }       means that if the survival funtion is printed every two years of age and if
      }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
    }       results. So we changed our mind and took the option of the best precision.
  if(mle==1){    */
     /* Computing hessian and covariance matrix */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     ftolhess=ftol; /* Usually correct */    agelim = AGESUP;
     hesscov(matcov, p, npar, delti, ftolhess, func);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  }      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     printf("# Scales (for hessian or gradient estimation)\n");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      for(i=1,jk=1; i <=nlstate; i++){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       for(j=1; j <=nlstate+ndeath; j++){      gp=matrix(0,nhstepm,1,nlstate);
         if (j!=i) {      gm=matrix(0,nhstepm,1,nlstate);
           fprintf(ficres,"%1d%1d",i,j);  
           printf("%1d%1d",i,j);  
           for(k=1; k<=ncovmodel;k++){      for(theta=1; theta <=npar; theta++){
             printf(" %.5e",delti[jk]);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
             fprintf(ficres," %.5e",delti[jk]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             jk++;        }
           }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           printf("\n");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           fprintf(ficres,"\n");  
         }        if (popbased==1) {
       }          if(mobilav ==0){
      }            for(i=1; i<=nlstate;i++)
                  prlim[i][i]=probs[(int)age][i][ij];
     k=1;          }else{ /* mobilav */ 
     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");            for(i=1; i<=nlstate;i++)
     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");              prlim[i][i]=mobaverage[(int)age][i][ij];
     for(i=1;i<=npar;i++){          }
       /*  if (k>nlstate) k=1;        }
       i1=(i-1)/(ncovmodel*nlstate)+1;    
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        for(j=1; j<= nlstate; j++){
       printf("%s%d%d",alph[k],i1,tab[i]);*/          for(h=0; h<=nhstepm; h++){
       fprintf(ficres,"%3d",i);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
       printf("%3d",i);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       for(j=1; j<=i;j++){          }
         fprintf(ficres," %.5e",matcov[i][j]);        }
         printf(" %.5e",matcov[i][j]);        /* This for computing probability of death (h=1 means
       }           computed over hstepm matrices product = hstepm*stepm months) 
       fprintf(ficres,"\n");           as a weighted average of prlim.
       printf("\n");        */
       k++;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
                gpp[j] += prlim[i][i]*p3mat[i][j][1];
     while((c=getc(ficpar))=='#' && c!= EOF){        }    
       ungetc(c,ficpar);        /* end probability of death */
       fgets(line, MAXLINE, ficpar);  
       puts(line);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       fputs(line,ficparo);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     ungetc(c,ficpar);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     estepm=0;   
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);        if (popbased==1) {
     if (estepm==0 || estepm < stepm) estepm=stepm;          if(mobilav ==0){
     if (fage <= 2) {            for(i=1; i<=nlstate;i++)
       bage = ageminpar;              prlim[i][i]=probs[(int)age][i][ij];
       fage = agemaxpar;          }else{ /* mobilav */ 
     }            for(i=1; i<=nlstate;i++)
                  prlim[i][i]=mobaverage[(int)age][i][ij];
     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);  
          for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
     while((c=getc(ficpar))=='#' && c!= EOF){          for(h=0; h<=nhstepm; h++){
     ungetc(c,ficpar);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     puts(line);          }
     fputs(line,ficparo);        }
   }        /* This for computing probability of death (h=1 means
   ungetc(c,ficpar);           computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        */
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
                 gmp[j] += prlim[i][i]*p3mat[i][j][1];
   while((c=getc(ficpar))=='#' && c!= EOF){        }    
     ungetc(c,ficpar);        /* end probability of death */
     fgets(line, MAXLINE, ficpar);  
     puts(line);        for(j=1; j<= nlstate; j++) /* vareij */
     fputs(line,ficparo);          for(h=0; h<=nhstepm; h++){
   }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   ungetc(c,ficpar);          }
    
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        }
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);      } /* End theta */
   fprintf(ficparo,"pop_based=%d\n",popbased);    
   fprintf(ficres,"pop_based=%d\n",popbased);        trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
    
   while((c=getc(ficpar))=='#' && c!= EOF){      for(h=0; h<=nhstepm; h++) /* veij */
     ungetc(c,ficpar);        for(j=1; j<=nlstate;j++)
     fgets(line, MAXLINE, ficpar);          for(theta=1; theta <=npar; theta++)
     puts(line);            trgradg[h][j][theta]=gradg[h][theta][j];
     fputs(line,ficparo);  
   }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   ungetc(c,ficpar);        for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
   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);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
 while((c=getc(ficpar))=='#' && c!= EOF){          vareij[i][j][(int)age] =0.;
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      for(h=0;h<=nhstepm;h++){
     puts(line);        for(k=0;k<=nhstepm;k++){
     fputs(line,ficparo);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   }          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   ungetc(c,ficpar);          for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        }
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      }
     
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
 /*------------ gnuplot -------------*/      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
          for(i=nlstate+1;i<=nlstate+ndeath;i++)
 /*------------ free_vector  -------------*/          varppt[j][i]=doldmp[j][i];
  chdir(path);      /* end ppptj */
        /*  x centered again */
  free_ivector(wav,1,imx);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);     
  free_ivector(num,1,n);      if (popbased==1) {
  free_vector(agedc,1,n);        if(mobilav ==0){
  /*free_matrix(covar,1,NCOVMAX,1,n);*/          for(i=1; i<=nlstate;i++)
  fclose(ficparo);            prlim[i][i]=probs[(int)age][i][ij];
  fclose(ficres);        }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
 /*--------- index.htm --------*/            prlim[i][i]=mobaverage[(int)age][i][ij];
         }
  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);      }
                
        /* This for computing probability of death (h=1 means
   /*--------------- Prevalence limit --------------*/         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           as a weighted average of prlim.
   strcpy(filerespl,"pl");      */
   strcat(filerespl,fileres);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   }      }    
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      /* end probability of death */
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   fprintf(ficrespl,"\n");        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
          for(i=1; i<=nlstate;i++){
   prlim=matrix(1,nlstate,1,nlstate);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   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 */      fprintf(ficresprobmorprev,"\n");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      fprintf(ficresvij,"%.0f ",age );
   k=0;      for(i=1; i<=nlstate;i++)
   agebase=ageminpar;        for(j=1; j<=nlstate;j++){
   agelim=agemaxpar;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   ftolpl=1.e-10;        }
   i1=cptcoveff;      fprintf(ficresvij,"\n");
   if (cptcovn < 1){i1=1;}      free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
   for(cptcov=1;cptcov<=i1;cptcov++){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
         k=k+1;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    } /* End age */
         fprintf(ficrespl,"\n#******");    free_vector(gpp,nlstate+1,nlstate+ndeath);
         for(j=1;j<=cptcoveff;j++)    free_vector(gmp,nlstate+1,nlstate+ndeath);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
         fprintf(ficrespl,"******\n");    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
            fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
         for (age=agebase; age<=agelim; age++){    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
           fprintf(ficrespl,"%.0f",age );  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           for(i=1; i<=nlstate;i++)  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
           fprintf(ficrespl," %.5f", prlim[i][i]);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
           fprintf(ficrespl,"\n");    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
         }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
       }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     }    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   fclose(ficrespl);    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);
   /*------------- h Pij x at various ages ------------*/  */
    /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    free_vector(xp,1,npar);
   }    free_matrix(doldm,1,nlstate,1,nlstate);
   printf("Computing pij: result on file '%s' \n", filerespij);    free_matrix(dnewm,1,nlstate,1,npar);
      free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   /*if (stepm<=24) stepsize=2;*/    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   agelim=AGESUP;    fclose(ficresprobmorprev);
   hstepm=stepsize*YEARM; /* Every year of age */    fflush(ficgp);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    fflush(fichtm); 
    }  /* end varevsij */
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){  /************ Variance of prevlim ******************/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  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[])
       k=k+1;  {
         fprintf(ficrespij,"\n#****** ");    /* Variance of prevalence limit */
         for(j=1;j<=cptcoveff;j++)    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double **newm;
         fprintf(ficrespij,"******\n");    double **dnewm,**doldm;
            int i, j, nhstepm, hstepm;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    int k, cptcode;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double *xp;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double *gp, *gm;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **gradg, **trgradg;
           oldm=oldms;savm=savms;    double age,agelim;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      int theta;
           fprintf(ficrespij,"# Age");    
           for(i=1; i<=nlstate;i++)    pstamp(ficresvpl);
             for(j=1; j<=nlstate+ndeath;j++)    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
               fprintf(ficrespij," %1d-%1d",i,j);    fprintf(ficresvpl,"# Age");
           fprintf(ficrespij,"\n");    for(i=1; i<=nlstate;i++)
            for (h=0; h<=nhstepm; h++){        fprintf(ficresvpl," %1d-%1d",i,i);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    fprintf(ficresvpl,"\n");
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)    xp=vector(1,npar);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    dnewm=matrix(1,nlstate,1,npar);
             fprintf(ficrespij,"\n");    doldm=matrix(1,nlstate,1,nlstate);
              }    
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    hstepm=1*YEARM; /* Every year of age */
           fprintf(ficrespij,"\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         }    agelim = AGESUP;
     }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   }      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
   fclose(ficrespij);      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
   /*---------- Forecasting ------------------*/      for(theta=1; theta <=npar; theta++){
   if((stepm == 1) && (strcmp(model,".")==0)){        for(i=1; i<=npar; i++){ /* Computes gradient */
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);        }
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   else{        for(i=1;i<=nlstate;i++)
     erreur=108;          gp[i] = prlim[i][i];
     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);      
   }        for(i=1; i<=npar; i++) /* Computes gradient */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /*---------- Health expectancies and variances ------------*/        for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   strcpy(filerest,"t");  
   strcat(filerest,fileres);        for(i=1;i<=nlstate;i++)
   if((ficrest=fopen(filerest,"w"))==NULL) {          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      } /* End theta */
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
   strcpy(filerese,"e");        for(theta=1; theta <=npar; theta++)
   strcat(filerese,fileres);          trgradg[j][theta]=gradg[theta][j];
   if((ficreseij=fopen(filerese,"w"))==NULL) {  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      for(i=1;i<=nlstate;i++)
   }        varpl[i][(int)age] =0.;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
  strcpy(fileresv,"v");      for(i=1;i<=nlstate;i++)
   strcat(fileresv,fileres);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      fprintf(ficresvpl,"%.0f ",age );
   }      for(i=1; i<=nlstate;i++)
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   calagedate=-1;      fprintf(ficresvpl,"\n");
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
   k=0;      free_matrix(gradg,1,npar,1,nlstate);
   for(cptcov=1;cptcov<=i1;cptcov++){      free_matrix(trgradg,1,nlstate,1,npar);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    } /* End age */
       k=k+1;  
       fprintf(ficrest,"\n#****** ");    free_vector(xp,1,npar);
       for(j=1;j<=cptcoveff;j++)    free_matrix(doldm,1,nlstate,1,npar);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    free_matrix(dnewm,1,nlstate,1,nlstate);
       fprintf(ficrest,"******\n");  
   }
       fprintf(ficreseij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)  /************ Variance of one-step probabilities  ******************/
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  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[])
       fprintf(ficreseij,"******\n");  {
     int i, j=0,  i1, k1, l1, t, tj;
       fprintf(ficresvij,"\n#****** ");    int k2, l2, j1,  z1;
       for(j=1;j<=cptcoveff;j++)    int k=0,l, cptcode;
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int first=1, first1, first2;
       fprintf(ficresvij,"******\n");    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double *xp;
       oldm=oldms;savm=savms;    double *gp, *gm;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      double **gradg, **trgradg;
      double **mu;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double age,agelim, cov[NCOVMAX+1];
       oldm=oldms;savm=savms;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    int theta;
        char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
      char fileresprobcor[FILENAMELENGTH];
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    double ***varpij;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");    strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
       epj=vector(1,nlstate+1);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       for(age=bage; age <=fage ;age++){      printf("Problem with resultfile: %s\n", fileresprob);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
         if (popbased==1) {    }
           for(i=1; i<=nlstate;i++)    strcpy(fileresprobcov,"probcov"); 
             prlim[i][i]=probs[(int)age][i][k];    strcat(fileresprobcov,fileres);
         }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
              printf("Problem with resultfile: %s\n", fileresprobcov);
         fprintf(ficrest," %4.0f",age);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    strcpy(fileresprobcor,"probcor"); 
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    strcat(fileresprobcor,fileres);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
           }      printf("Problem with resultfile: %s\n", fileresprobcor);
           epj[nlstate+1] +=epj[j];      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
         }    }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         for(i=1, vepp=0.;i <=nlstate;i++)    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           for(j=1;j <=nlstate;j++)    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
             vepp += vareij[i][j][(int)age];    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         for(j=1;j <=nlstate;j++){    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    pstamp(ficresprob);
         }    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
         fprintf(ficrest,"\n");    fprintf(ficresprob,"# Age");
       }    pstamp(ficresprobcov);
     }    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   }    fprintf(ficresprobcov,"# Age");
 free_matrix(mint,1,maxwav,1,n);    pstamp(ficresprobcor);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     free_vector(weight,1,n);    fprintf(ficresprobcor,"# Age");
   fclose(ficreseij);  
   fclose(ficresvij);  
   fclose(ficrest);    for(i=1; i<=nlstate;i++)
   fclose(ficpar);      for(j=1; j<=(nlstate+ndeath);j++){
   free_vector(epj,1,nlstate+1);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
          fprintf(ficresprobcov," p%1d-%1d ",i,j);
   /*------- Variance limit prevalence------*/          fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
   strcpy(fileresvpl,"vpl");   /* fprintf(ficresprob,"\n");
   strcat(fileresvpl,fileres);    fprintf(ficresprobcov,"\n");
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    fprintf(ficresprobcor,"\n");
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);   */
     exit(0);    xp=vector(1,npar);
   }    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   k=0;    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   for(cptcov=1;cptcov<=i1;cptcov++){    first=1;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficgp,"\n# Routine varprob");
       k=k+1;    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       fprintf(ficresvpl,"\n#****** ");    fprintf(fichtm,"\n");
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
       fprintf(ficresvpl,"******\n");    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
          file %s<br>\n",optionfilehtmcov);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
       oldm=oldms;savm=savms;  and drawn. It helps understanding how is the covariance between two incidences.\
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);   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 \
   fclose(ficresvpl);  standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   /*---------- End : free ----------------*/   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    cov[1]=1;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    /* tj=cptcoveff; */
      tj = (int) pow(2,cptcoveff);
      if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    j1=0;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    for(j1=1; j1<=tj;j1++){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      /*for(i1=1; i1<=ncodemax[t];i1++){ */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      /*j1++;*/
          if  (cptcovn>0) {
   free_matrix(matcov,1,npar,1,npar);          fprintf(ficresprob, "\n#********** Variable "); 
   free_vector(delti,1,npar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   free_matrix(agev,1,maxwav,1,imx);          fprintf(ficresprob, "**********\n#\n");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if(erreur >0)          fprintf(ficresprobcov, "**********\n#\n");
     printf("End of Imach with error or warning %d\n",erreur);          
   else   printf("End of Imach\n");          fprintf(ficgp, "\n#********** Variable "); 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficgp, "**********\n#\n");
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/          
   /*printf("Total time was %d uSec.\n", total_usecs);*/          
   /*------ End -----------*/          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\">");
  end:          
 #ifdef windows          fprintf(ficresprobcor, "\n#********** Variable ");    
   /* chdir(pathcd);*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 #endif          fprintf(ficresprobcor, "**********\n#");    
  /*system("wgnuplot graph.plt");*/        }
  /*system("../gp37mgw/wgnuplot graph.plt");*/        
  /*system("cd ../gp37mgw");*/        gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
  strcpy(plotcmd,GNUPLOTPROGRAM);        gp=vector(1,(nlstate)*(nlstate+ndeath));
  strcat(plotcmd," ");        gm=vector(1,(nlstate)*(nlstate+ndeath));
  strcat(plotcmd,optionfilegnuplot);        for (age=bage; age<=fage; age ++){ 
  system(plotcmd);          cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
 #ifdef windows            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
   while (z[0] != 'q') {                                                           * 1  1 1 1 1
     /* chdir(path); */                                                           * 2  2 1 1 1
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");                                                           * 3  1 2 1 1
     scanf("%s",z);                                                           */
     if (z[0] == 'c') system("./imach");            /* nbcode[1][1]=0 nbcode[1][2]=1;*/
     else if (z[0] == 'e') system(optionfilehtm);          }
     else if (z[0] == 'g') system(plotcmd);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     else if (z[0] == 'q') exit(0);          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]]];
 #endif          
 }      
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    avoid:
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int i1, j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.46  
changed lines
  Added in v.1.145


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