Diff for /imach/src/imach.c between versions 1.41 and 1.156

version 1.41, 2002/05/07 15:53:01 version 1.156, 2014/08/25 20:10:10
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.156  2014/08/25 20:10:10  brouard
      *** empty log message ***
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.155  2014/08/25 18:32:34  brouard
   first survey ("cross") where individuals from different ages are    Summary: New compile, minor changes
   interviewed on their health status or degree of disability (in the    Author: Brouard
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.154  2014/06/20 17:32:08  brouard
   (if any) in individual health status.  Health expectancies are    Summary: Outputs now all graphs of convergence to period prevalence
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    Revision 1.153  2014/06/20 16:45:46  brouard
   Maximum Likelihood of the parameters involved in the model.  The    Summary: If 3 live state, convergence to period prevalence on same graph
   simplest model is the multinomial logistic model where pij is the    Author: Brouard
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.152  2014/06/18 17:54:09  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Summary: open browser, use gnuplot on same dir than imach if not found in the path
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.151  2014/06/18 16:43:30  brouard
   where the markup *Covariates have to be included here again* invites    *** empty log message ***
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.150  2014/06/18 16:42:35  brouard
     Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
   The advantage of this computer programme, compared to a simple    Author: brouard
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.149  2014/06/18 15:51:14  brouard
   intermediate interview, the information is lost, but taken into    Summary: Some fixes in parameter files errors
   account using an interpolation or extrapolation.      Author: Nicolas Brouard
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.148  2014/06/17 17:38:48  brouard
   conditional to the observed state i at age x. The delay 'h' can be    Summary: Nothing new
   split into an exact number (nh*stepm) of unobserved intermediate    Author: Brouard
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Just a new packaging for OS/X version 0.98nS
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.147  2014/06/16 10:33:11  brouard
   hPijx.    *** empty log message ***
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.146  2014/06/16 10:20:28  brouard
   of the life expectancies. It also computes the prevalence limits.    Summary: Merge
      Author: Brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Merge, before building revised version.
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.145  2014/06/10 21:23:15  brouard
   It is copyrighted identically to a GNU software product, ie programme and    Summary: Debugging with valgrind
   software can be distributed freely for non commercial use. Latest version    Author: Nicolas Brouard
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Lot of changes in order to output the results with some covariates
      After the Edimburgh REVES conference 2014, it seems mandatory to
 #include <math.h>    improve the code.
 #include <stdio.h>    No more memory valgrind error but a lot has to be done in order to
 #include <stdlib.h>    continue the work of splitting the code into subroutines.
 #include <unistd.h>    Also, decodemodel has been improved. Tricode is still not
     optimal. nbcode should be improved. Documentation has been added in
 #define MAXLINE 256    the source code.
 #define GNUPLOTPROGRAM "wgnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.143  2014/01/26 09:45:38  brouard
 #define FILENAMELENGTH 80    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 /*#define DEBUG*/  
 #define windows    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.142  2014/01/26 03:57:36  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.141  2014/01/26 02:42:01  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.140  2011/09/02 10:37:54  brouard
 #define YEARM 12. /* Number of months per year */    Summary: times.h is ok with mingw32 now.
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.139  2010/06/14 07:50:17  brouard
     After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
     I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 int erreur; /* Error number */  
 int nvar;    Revision 1.138  2010/04/30 18:19:40  brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    *** empty log message ***
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.137  2010/04/29 18:11:38  brouard
 int ndeath=1; /* Number of dead states */    (Module): Checking covariates for more complex models
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    than V1+V2. A lot of change to be done. Unstable.
 int popbased=0;  
     Revision 1.136  2010/04/26 20:30:53  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): merging some libgsl code. Fixing computation
 int maxwav; /* Maxim number of waves */    of likelione (using inter/intrapolation if mle = 0) in order to
 int jmin, jmax; /* min, max spacing between 2 waves */    get same likelihood as if mle=1.
 int mle, weightopt;    Some cleaning of code and comments added.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.135  2009/10/29 15:33:14  brouard
 double jmean; /* Mean space between 2 waves */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.134  2009/10/29 13:18:53  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 FILE *ficgp,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.133  2009/07/06 10:21:25  brouard
   char filerese[FILENAMELENGTH];    just nforces
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.132  2009/07/06 08:22:05  brouard
  FILE  *ficresvpl;    Many tings
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.131  2009/06/20 16:22:47  brouard
 #define NR_END 1    Some dimensions resccaled
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
 #define NRANSI    lot of cleaning with variables initialized to 0. Trying to make
 #define ITMAX 200    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
 #define TOL 2.0e-4    Revision 1.129  2007/08/31 13:49:27  lievre
     Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.128  2006/06/30 13:02:05  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    (Module): Clarifications on computing e.j
   
 #define GOLD 1.618034    Revision 1.127  2006/04/28 18:11:50  brouard
 #define GLIMIT 100.0    (Module): Yes the sum of survivors was wrong since
 #define TINY 1.0e-20    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
 static double maxarg1,maxarg2;    (Module): In order to speed up (in case of numerous covariates) we
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    compute health expectancies (without variances) in a first step
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    and then all the health expectancies with variances or standard
      deviation (needs data from the Hessian matrices) which slows the
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    computation.
 #define rint(a) floor(a+0.5)    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.126  2006/04/28 17:23:28  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 int imx;    loop. Now we define nhstepma in the age loop.
 int stepm;    Version 0.98h
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.125  2006/04/04 15:20:31  lievre
 int estepm;    Errors in calculation of health expectancies. Age was not initialized.
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Forecasting file added.
   
 int m,nb;    Revision 1.124  2006/03/22 17:13:53  lievre
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Parameters are printed with %lf instead of %f (more numbers after the comma).
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    The log-likelihood is printed in the log file
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    Revision 1.123  2006/03/20 10:52:43  brouard
     * imach.c (Module): <title> changed, corresponds to .htm file
 double *weight;    name. <head> headers where missing.
 int **s; /* Status */  
 double *agedc, **covar, idx;    * imach.c (Module): Weights can have a decimal point as for
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Modification of warning when the covariates values are not 0 or
 double ftolhess; /* Tolerance for computing hessian */    1.
     Version 0.98g
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.122  2006/03/20 09:45:41  brouard
 {    (Module): Weights can have a decimal point as for
    char *s;                             /* pointer */    English (a comma might work with a correct LC_NUMERIC environment,
    int  l1, l2;                         /* length counters */    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
    l1 = strlen( path );                 /* length of path */    1.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Version 0.98g
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.121  2006/03/16 17:45:01  lievre
 #else    * imach.c (Module): Comments concerning covariates added
    s = strrchr( path, '/' );            /* find last / */  
 #endif    * imach.c (Module): refinements in the computation of lli if
    if ( s == NULL ) {                   /* no directory, so use current */    status=-2 in order to have more reliable computation if stepm is
 #if     defined(__bsd__)                /* get current working directory */    not 1 month. Version 0.98f
       extern char       *getwd( );  
     Revision 1.120  2006/03/16 15:10:38  lievre
       if ( getwd( dirc ) == NULL ) {    (Module): refinements in the computation of lli if
 #else    status=-2 in order to have more reliable computation if stepm is
       extern char       *getcwd( );    not 1 month. Version 0.98f
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.119  2006/03/15 17:42:26  brouard
 #endif    (Module): Bug if status = -2, the loglikelihood was
          return( GLOCK_ERROR_GETCWD );    computed as likelihood omitting the logarithm. Version O.98e
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.118  2006/03/14 18:20:07  brouard
    } else {                             /* strip direcotry from path */    (Module): varevsij Comments added explaining the second
       s++;                              /* after this, the filename */    table of variances if popbased=1 .
       l2 = strlen( s );                 /* length of filename */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): Function pstamp added
       strcpy( name, s );                /* save file name */    (Module): Version 0.98d
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.117  2006/03/14 17:16:22  brouard
    }    (Module): varevsij Comments added explaining the second
    l1 = strlen( dirc );                 /* length of directory */    table of variances if popbased=1 .
 #ifdef windows    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    (Module): Function pstamp added
 #else    (Module): Version 0.98d
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.116  2006/03/06 10:29:27  brouard
    s = strrchr( name, '.' );            /* find last / */    (Module): Variance-covariance wrong links and
    s++;    varian-covariance of ej. is needed (Saito).
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Revision 1.115  2006/02/27 12:17:45  brouard
    l2= strlen( s)+1;    (Module): One freematrix added in mlikeli! 0.98c
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.114  2006/02/26 12:57:58  brouard
    return( 0 );                         /* we're done */    (Module): Some improvements in processing parameter
 }    filename with strsep.
   
     Revision 1.113  2006/02/24 14:20:24  brouard
 /******************************************/    (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
 void replace(char *s, char*t)    allocation too.
 {  
   int i;    Revision 1.112  2006/01/30 09:55:26  brouard
   int lg=20;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   i=0;  
   lg=strlen(t);    Revision 1.111  2006/01/25 20:38:18  brouard
   for(i=0; i<= lg; i++) {    (Module): Lots of cleaning and bugs added (Gompertz)
     (s[i] = t[i]);    (Module): Comments can be added in data file. Missing date values
     if (t[i]== '\\') s[i]='/';    can be a simple dot '.'.
   }  
 }    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 int nbocc(char *s, char occ)  
 {    Revision 1.109  2006/01/24 19:37:15  brouard
   int i,j=0;    (Module): Comments (lines starting with a #) are allowed in data.
   int lg=20;  
   i=0;    Revision 1.108  2006/01/19 18:05:42  lievre
   lg=strlen(s);    Gnuplot problem appeared...
   for(i=0; i<= lg; i++) {    To be fixed
   if  (s[i] == occ ) j++;  
   }    Revision 1.107  2006/01/19 16:20:37  brouard
   return j;    Test existence of gnuplot in imach path
 }  
     Revision 1.106  2006/01/19 13:24:36  brouard
 void cutv(char *u,char *v, char*t, char occ)    Some cleaning and links added in html output
 {  
   int i,lg,j,p=0;    Revision 1.105  2006/01/05 20:23:19  lievre
   i=0;    *** empty log message ***
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Revision 1.104  2005/09/30 16:11:43  lievre
   }    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
   lg=strlen(t);    that the person is alive, then we can code his/her status as -2
   for(j=0; j<p; j++) {    (instead of missing=-1 in earlier versions) and his/her
     (u[j] = t[j]);    contributions to the likelihood is 1 - Prob of dying from last
   }    health status (= 1-p13= p11+p12 in the easiest case of somebody in
      u[p]='\0';    the healthy state at last known wave). Version is 0.98
   
    for(j=0; j<= lg; j++) {    Revision 1.103  2005/09/30 15:54:49  lievre
     if (j>=(p+1))(v[j-p-1] = t[j]);    (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.
 /********************** nrerror ********************/  
     Revision 1.101  2004/09/15 10:38:38  brouard
 void nrerror(char error_text[])    Fix on curr_time
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.100  2004/07/12 18:29:06  brouard
   fprintf(stderr,"%s\n",error_text);    Add version for Mac OS X. Just define UNIX in Makefile
   exit(1);  
 }    Revision 1.99  2004/06/05 08:57:40  brouard
 /*********************** vector *******************/    *** empty log message ***
 double *vector(int nl, int nh)  
 {    Revision 1.98  2004/05/16 15:05:56  brouard
   double *v;    New version 0.97 . First attempt to estimate force of mortality
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    directly from the data i.e. without the need of knowing the health
   if (!v) nrerror("allocation failure in vector");    state at each age, but using a Gompertz model: log u =a + b*age .
   return v-nl+NR_END;    This is the basic analysis of mortality and should be done before any
 }    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
 /************************ free vector ******************/    from other sources like vital statistic data.
 void free_vector(double*v, int nl, int nh)  
 {    The same imach parameter file can be used but the option for mle should be -3.
   free((FREE_ARG)(v+nl-NR_END));  
 }    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.
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    The output is very simple: only an estimate of the intercept and of
 {    the slope with 95% confident intervals.
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Current limitations:
   if (!v) nrerror("allocation failure in ivector");    A) Even if you enter covariates, i.e. with the
   return v-nl+NR_END;    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.
   
 /******************free ivector **************************/    Revision 1.97  2004/02/20 13:25:42  lievre
 void free_ivector(int *v, long nl, long nh)    Version 0.96d. Population forecasting command line is (temporarily)
 {    suppressed.
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 /******************* imatrix *******************************/    rewritten within the same printf. Workaround: many printfs.
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Revision 1.95  2003/07/08 07:54:34  brouard
 {    * imach.c (Repository):
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    (Repository): Using imachwizard code to output a more meaningful covariance
   int **m;    matrix (cov(a12,c31) instead of numbers.
    
   /* allocate pointers to rows */    Revision 1.94  2003/06/27 13:00:02  brouard
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Just cleaning
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.93  2003/06/25 16:33:55  brouard
   m -= nrl;    (Module): On windows (cygwin) function asctime_r doesn't
      exist so I changed back to asctime which exists.
      (Module): Version 0.96b
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Revision 1.92  2003/06/25 16:30:45  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Module): On windows (cygwin) function asctime_r doesn't
   m[nrl] += NR_END;    exist so I changed back to asctime which exists.
   m[nrl] -= ncl;  
      Revision 1.91  2003/06/25 15:30:29  brouard
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    * imach.c (Repository): Duplicated warning errors corrected.
      (Repository): Elapsed time after each iteration is now output. It
   /* return pointer to array of pointers to rows */    helps to forecast when convergence will be reached. Elapsed time
   return m;    is stamped in powell.  We created a new html file for the graphs
 }    concerning matrix of covariance. It has extension -cov.htm.
   
 /****************** free_imatrix *************************/    Revision 1.90  2003/06/24 12:34:15  brouard
 void free_imatrix(m,nrl,nrh,ncl,nch)    (Module): Some bugs corrected for windows. Also, when
       int **m;    mle=-1 a template is output in file "or"mypar.txt with the design
       long nch,ncl,nrh,nrl;    of the covariance matrix to be input.
      /* free an int matrix allocated by imatrix() */  
 {    Revision 1.89  2003/06/24 12:30:52  brouard
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    (Module): Some bugs corrected for windows. Also, when
   free((FREE_ARG) (m+nrl-NR_END));    mle=-1 a template is output in file "or"mypar.txt with the design
 }    of the covariance matrix to be input.
   
 /******************* matrix *******************************/    Revision 1.88  2003/06/23 17:54:56  brouard
 double **matrix(long nrl, long nrh, long ncl, long nch)    * 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.
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    Revision 1.87  2003/06/18 12:26:01  brouard
   double **m;    Version 0.96
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.86  2003/06/17 20:04:08  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Change position of html and gnuplot routines and added
   m += NR_END;    routine fileappend.
   m -= nrl;  
     Revision 1.85  2003/06/17 13:12:43  brouard
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    * imach.c (Repository): Check when date of death was earlier that
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    current date of interview. It may happen when the death was just
   m[nrl] += NR_END;    prior to the death. In this case, dh was negative and likelihood
   m[nrl] -= ncl;    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    interview.
   return m;    (Repository): Because some people have very long ID (first column)
 }    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
 /*************************free matrix ************************/    truncation)
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    (Repository): No more line truncation errors.
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Revision 1.84  2003/06/13 21:44:43  brouard
   free((FREE_ARG)(m+nrl-NR_END));    * imach.c (Repository): Replace "freqsummary" at a correct
 }    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
 /******************* ma3x *******************************/    parcimony.
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Revision 1.83  2003/06/10 13:39:11  lievre
   double ***m;    *** empty log message ***
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.82  2003/06/05 15:57:20  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    Add log in  imach.c and  fullversion number is now printed.
   m += NR_END;  
   m -= nrl;  */
   /*
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));     Interpolated Markov Chain
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Short summary of the programme:
   m[nrl] -= ncl;    
     This program computes Healthy Life Expectancies from
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    interviewed on their health status or degree of disability (in the
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    case of a health survey which is our main interest) -2- at least a
   m[nrl][ncl] += NR_END;    second wave of interviews ("longitudinal") which measure each change
   m[nrl][ncl] -= nll;    (if any) in individual health status.  Health expectancies are
   for (j=ncl+1; j<=nch; j++)    computed from the time spent in each health state according to a
     m[nrl][j]=m[nrl][j-1]+nlay;    model. More health states you consider, more time is necessary to reach the
      Maximum Likelihood of the parameters involved in the model.  The
   for (i=nrl+1; i<=nrh; i++) {    simplest model is the multinomial logistic model where pij is the
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    probability to be observed in state j at the second wave
     for (j=ncl+1; j<=nch; j++)    conditional to be observed in state i at the first wave. Therefore
       m[i][j]=m[i][j-1]+nlay;    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
   return m;    complex model than "constant and age", you should modify the program
 }    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 /*************************free ma3x ************************/    convergence.
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {    The advantage of this computer programme, compared to a simple
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    multinomial logistic model, is clear when the delay between waves is not
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    identical for each individual. Also, if a individual missed an
   free((FREE_ARG)(m+nrl-NR_END));    intermediate interview, the information is lost, but taken into
 }    account using an interpolation or extrapolation.  
   
 /***************** f1dim *************************/    hPijx is the probability to be observed in state i at age x+h
 extern int ncom;    conditional to the observed state i at age x. The delay 'h' can be
 extern double *pcom,*xicom;    split into an exact number (nh*stepm) of unobserved intermediate
 extern double (*nrfunc)(double []);    states. This elementary transition (by month, quarter,
      semester or year) is modelled as a multinomial logistic.  The hPx
 double f1dim(double x)    matrix is simply the matrix product of nh*stepm elementary matrices
 {    and the contribution of each individual to the likelihood is simply
   int j;    hPijx.
   double f;  
   double *xt;    Also this programme outputs the covariance matrix of the parameters but also
      of the life expectancies. It also computes the period (stable) prevalence. 
   xt=vector(1,ncom);    
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   f=(*nrfunc)(xt);             Institut national d'études démographiques, Paris.
   free_vector(xt,1,ncom);    This software have been partly granted by Euro-REVES, a concerted action
   return f;    from the European Union.
 }    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 /*****************brent *************************/    can be accessed at http://euroreves.ined.fr/imach .
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   int iter;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   double a,b,d,etemp;    
   double fu,fv,fw,fx;    **********************************************************************/
   double ftemp;  /*
   double p,q,r,tol1,tol2,u,v,w,x,xm;    main
   double e=0.0;    read parameterfile
      read datafile
   a=(ax < cx ? ax : cx);    concatwav
   b=(ax > cx ? ax : cx);    freqsummary
   x=w=v=bx;    if (mle >= 1)
   fw=fv=fx=(*f)(x);      mlikeli
   for (iter=1;iter<=ITMAX;iter++) {    print results files
     xm=0.5*(a+b);    if mle==1 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);       computes hessian
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    read end of parameter file: agemin, agemax, bage, fage, estepm
     printf(".");fflush(stdout);        begin-prev-date,...
 #ifdef DEBUG    open gnuplot file
     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);    open html file
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
 #endif     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
       *xmin=x;      freexexit2 possible for memory heap.
       return fx;  
     }    h Pij x                         | pij_nom  ficrestpij
     ftemp=fu;     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
     if (fabs(e) > tol1) {         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
       r=(x-w)*(fx-fv);         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
       q=2.0*(q-r);         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
       if (q > 0.0) p = -p;    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
       q=fabs(q);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
       etemp=e;     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    forecasting if prevfcast==1 prevforecast call prevalence()
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    health expectancies
       else {    Variance-covariance of DFLE
         d=p/q;    prevalence()
         u=x+d;     movingaverage()
         if (u-a < tol2 || b-u < tol2)    varevsij() 
           d=SIGN(tol1,xm-x);    if popbased==1 varevsij(,popbased)
       }    total life expectancies
     } else {    Variance of period (stable) prevalence
       d=CGOLD*(e=(x >= xm ? a-x : b-x));   end
     }  */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;   
       SHFT(v,w,x,u)  #include <math.h>
         SHFT(fv,fw,fx,fu)  #include <stdio.h>
         } else {  #include <stdlib.h>
           if (u < x) a=u; else b=u;  #include <string.h>
           if (fu <= fw || w == x) {  #include <unistd.h>
             v=w;  
             w=u;  #include <limits.h>
             fv=fw;  #include <sys/types.h>
             fw=fu;  #include <sys/stat.h>
           } else if (fu <= fv || v == x || v == w) {  #include <errno.h>
             v=u;  extern int errno;
             fv=fu;  
           }  #ifdef LINUX
         }  #include <time.h>
   }  #include "timeval.h"
   nrerror("Too many iterations in brent");  #else
   *xmin=x;  #include <sys/time.h>
   return fx;  #endif
 }  
   #ifdef GSL
 /****************** mnbrak ***********************/  #include <gsl/gsl_errno.h>
   #include <gsl/gsl_multimin.h>
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #endif
             double (*func)(double))  
 {  /* #include <libintl.h> */
   double ulim,u,r,q, dum;  /* #define _(String) gettext (String) */
   double fu;  
    #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);  #define GNUPLOTPROGRAM "gnuplot"
   if (*fb > *fa) {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     SHFT(dum,*ax,*bx,dum)  #define FILENAMELENGTH 132
       SHFT(dum,*fb,*fa,dum)  
       }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   *cx=(*bx)+GOLD*(*bx-*ax);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
     r=(*bx-*ax)*(*fb-*fc);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #define NINTERVMAX 8
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
     if ((*bx-u)*(u-*cx) > 0.0) {  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
       fu=(*func)(u);  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define MAXN 20000
       fu=(*func)(u);  #define YEARM 12. /**< Number of months per year */
       if (fu < *fc) {  #define AGESUP 130
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define AGEBASE 40
           SHFT(*fb,*fc,fu,(*func)(u))  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
           }  #ifdef UNIX
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  #define DIRSEPARATOR '/'
       u=ulim;  #define CHARSEPARATOR "/"
       fu=(*func)(u);  #define ODIRSEPARATOR '\\'
     } else {  #else
       u=(*cx)+GOLD*(*cx-*bx);  #define DIRSEPARATOR '\\'
       fu=(*func)(u);  #define CHARSEPARATOR "\\"
     }  #define ODIRSEPARATOR '/'
     SHFT(*ax,*bx,*cx,u)  #endif
       SHFT(*fa,*fb,*fc,fu)  
       }  /* $Id$ */
 }  /* $State$ */
   
 /*************** linmin ************************/  char version[]="Imach version 0.98nV, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
   char fullversion[]="$Revision$ $Date$"; 
 int ncom;  char strstart[80];
 double *pcom,*xicom;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 double (*nrfunc)(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 */
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
 {  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   double brent(double ax, double bx, double cx,  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
                double (*f)(double), double tol, double *xmin);  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
   double f1dim(double x);  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  int cptcovprodnoage=0; /**< Number of covariate products without age */   
               double *fc, double (*func)(double));  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   int j;  int cptcov=0; /* Working variable */
   double xx,xmin,bx,ax;  int npar=NPARMAX;
   double fx,fb,fa;  int nlstate=2; /* Number of live states */
    int ndeath=1; /* Number of dead states */
   ncom=n;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   pcom=vector(1,n);  int popbased=0;
   xicom=vector(1,n);  
   nrfunc=func;  int *wav; /* Number of waves for this individuual 0 is possible */
   for (j=1;j<=n;j++) {  int maxwav=0; /* Maxim number of waves */
     pcom[j]=p[j];  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     xicom[j]=xi[j];  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   }  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   ax=0.0;                     to the likelihood and the sum of weights (done by funcone)*/
   xx=1.0;  int mle=1, weightopt=0;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 #ifdef DEBUG  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 #endif  double jmean=1; /* Mean space between 2 waves */
   for (j=1;j<=n;j++) {  double **matprod2(); /* test */
     xi[j] *= xmin;  double **oldm, **newm, **savm; /* Working pointers to matrices */
     p[j] += xi[j];  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   }  /*FILE *fic ; */ /* Used in readdata only */
   free_vector(xicom,1,n);  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   free_vector(pcom,1,n);  FILE *ficlog, *ficrespow;
 }  int globpr=0; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
 /*************** powell ************************/  long ipmx=0; /* Number of contributions */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  double sw; /* Sum of weights */
             double (*func)(double []))  char filerespow[FILENAMELENGTH];
 {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   void linmin(double p[], double xi[], int n, double *fret,  FILE *ficresilk;
               double (*func)(double []));  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   int i,ibig,j;  FILE *ficresprobmorprev;
   double del,t,*pt,*ptt,*xit;  FILE *fichtm, *fichtmcov; /* Html File */
   double fp,fptt;  FILE *ficreseij;
   double *xits;  char filerese[FILENAMELENGTH];
   pt=vector(1,n);  FILE *ficresstdeij;
   ptt=vector(1,n);  char fileresstde[FILENAMELENGTH];
   xit=vector(1,n);  FILE *ficrescveij;
   xits=vector(1,n);  char filerescve[FILENAMELENGTH];
   *fret=(*func)(p);  FILE  *ficresvij;
   for (j=1;j<=n;j++) pt[j]=p[j];  char fileresv[FILENAMELENGTH];
   for (*iter=1;;++(*iter)) {  FILE  *ficresvpl;
     fp=(*fret);  char fileresvpl[FILENAMELENGTH];
     ibig=0;  char title[MAXLINE];
     del=0.0;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     for (i=1;i<=n;i++)  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       printf(" %d %.12f",i, p[i]);  char command[FILENAMELENGTH];
     printf("\n");  int  outcmd=0;
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       fptt=(*fret);  
 #ifdef DEBUG  char filelog[FILENAMELENGTH]; /* Log file */
       printf("fret=%lf \n",*fret);  char filerest[FILENAMELENGTH];
 #endif  char fileregp[FILENAMELENGTH];
       printf("%d",i);fflush(stdout);  char popfile[FILENAMELENGTH];
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
         del=fabs(fptt-(*fret));  
         ibig=i;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
       }  struct timezone tzp;
 #ifdef DEBUG  extern int gettimeofday();
       printf("%d %.12e",i,(*fret));  struct tm tmg, tm, tmf, *gmtime(), *localtime();
       for (j=1;j<=n;j++) {  long time_value;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  extern long time();
         printf(" x(%d)=%.12e",j,xit[j]);  char strcurr[80], strfor[80];
       }  
       for(j=1;j<=n;j++)  char *endptr;
         printf(" p=%.12e",p[j]);  long lval;
       printf("\n");  double dval;
 #endif  
     }  #define NR_END 1
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #define FREE_ARG char*
 #ifdef DEBUG  #define FTOL 1.0e-10
       int k[2],l;  
       k[0]=1;  #define NRANSI 
       k[1]=-1;  #define ITMAX 200 
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)  #define TOL 2.0e-4 
         printf(" %.12e",p[j]);  
       printf("\n");  #define CGOLD 0.3819660 
       for(l=0;l<=1;l++) {  #define ZEPS 1.0e-10 
         for (j=1;j<=n;j++) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
           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]);  #define GOLD 1.618034 
         }  #define GLIMIT 100.0 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  #define TINY 1.0e-20 
       }  
 #endif  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       free_vector(xit,1,n);    
       free_vector(xits,1,n);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       free_vector(ptt,1,n);  #define rint(a) floor(a+0.5)
       free_vector(pt,1,n);  
       return;  static double sqrarg;
     }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     for (j=1;j<=n;j++) {  int agegomp= AGEGOMP;
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];  int imx; 
       pt[j]=p[j];  int stepm=1;
     }  /* Stepm, step in month: minimum step interpolation*/
     fptt=(*func)(ptt);  
     if (fptt < fp) {  int estepm;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  int m,nb;
         for (j=1;j<=n;j++) {  long *num;
           xi[j][ibig]=xi[j][n];  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
           xi[j][n]=xit[j];  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
         }  double **pmmij, ***probs;
 #ifdef DEBUG  double *ageexmed,*agecens;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  double dateintmean=0;
         for(j=1;j<=n;j++)  
           printf(" %.12e",xit[j]);  double *weight;
         printf("\n");  int **s; /* Status */
 #endif  double *agedc;
       }  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
     }                    * covar=matrix(0,NCOVMAX,1,n); 
   }                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
 }  double  idx; 
   int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
 /**** Prevalence limit ****************/  int *Ndum; /** Freq of modality (tricode */
   int **codtab; /**< codtab=imatrix(1,100,1,10); */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
 {  double *lsurv, *lpop, *tpop;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   double ftolhess; /**< Tolerance for computing hessian */
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;  /**************** split *************************/
   double **matprod2();  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   double **out, cov[NCOVMAX], **pmij();  {
   double **newm;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   double agefin, delaymax=50 ; /* Max number of years to converge */       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     */ 
   for (ii=1;ii<=nlstate+ndeath;ii++)    char  *ss;                            /* pointer */
     for (j=1;j<=nlstate+ndeath;j++){    int   l1, l2;                         /* length counters */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
     }    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
    cov[1]=1.;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
      if ( ss == NULL ) {                   /* no directory, so determine current directory */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      strcpy( name, path );               /* we got the fullname name because no directory */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     newm=savm;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     /* Covariates have to be included here again */      /* get current working directory */
      cov[2]=agefin;      /*    extern  char* getcwd ( char *buf , int len);*/
        if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       for (k=1; k<=cptcovn;k++) {        return( GLOCK_ERROR_GETCWD );
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      }
         /*      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]]);*/      /* got dirc from getcwd*/
       }      printf(" DIRC = %s \n",dirc);
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    } else {                              /* strip direcotry from path */
       for (k=1; k<=cptcovprod;k++)      ss++;                               /* after this, the filename */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      strcpy( name, ss );         /* save file name */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      dirc[l1-l2] = 0;                    /* add zero */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      printf(" DIRC2 = %s \n",dirc);
     }
     savm=oldm;    /* We add a separator at the end of dirc if not exists */
     oldm=newm;    l1 = strlen( dirc );                  /* length of directory */
     maxmax=0.;    if( dirc[l1-1] != DIRSEPARATOR ){
     for(j=1;j<=nlstate;j++){      dirc[l1] =  DIRSEPARATOR;
       min=1.;      dirc[l1+1] = 0; 
       max=0.;      printf(" DIRC3 = %s \n",dirc);
       for(i=1; i<=nlstate; i++) {    }
         sumnew=0;    ss = strrchr( name, '.' );            /* find last / */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    if (ss >0){
         prlim[i][j]= newm[i][j]/(1-sumnew);      ss++;
         max=FMAX(max,prlim[i][j]);      strcpy(ext,ss);                     /* save extension */
         min=FMIN(min,prlim[i][j]);      l1= strlen( name);
       }      l2= strlen(ss)+1;
       maxmin=max-min;      strncpy( finame, name, l1-l2);
       maxmax=FMAX(maxmax,maxmin);      finame[l1-l2]= 0;
     }    }
     if(maxmax < ftolpl){  
       return prlim;    return( 0 );                          /* we're done */
     }  }
   }  
 }  
   /******************************************/
 /*************** transition probabilities ***************/  
   void replace_back_to_slash(char *s, char*t)
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  {
 {    int i;
   double s1, s2;    int lg=0;
   /*double t34;*/    i=0;
   int i,j,j1, nc, ii, jj;    lg=strlen(t);
     for(i=0; i<= lg; i++) {
     for(i=1; i<= nlstate; i++){      (s[i] = t[i]);
     for(j=1; j<i;j++){      if (t[i]== '\\') s[i]='/';
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    }
         /*s2 += param[i][j][nc]*cov[nc];*/  }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  char *trimbb(char *out, char *in)
       }  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
       ps[i][j]=s2;    char *s;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    s=out;
     }    while (*in != '\0'){
     for(j=i+1; j<=nlstate+ndeath;j++){      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        in++;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      }
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      *out++ = *in++;
       }    }
       ps[i][j]=s2;    *out='\0';
     }    return s;
   }  }
     /*ps[3][2]=1;*/  
   char *cutl(char *blocc, char *alocc, char *in, char occ)
   for(i=1; i<= nlstate; i++){  {
      s1=0;    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
     for(j=1; j<i; j++)       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       s1+=exp(ps[i][j]);       gives blocc="abcdef2ghi" and alocc="j".
     for(j=i+1; j<=nlstate+ndeath; j++)       If occ is not found blocc is null and alocc is equal to in. Returns blocc
       s1+=exp(ps[i][j]);    */
     ps[i][i]=1./(s1+1.);    char *s, *t, *bl;
     for(j=1; j<i; j++)    t=in;s=in;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    while ((*in != occ) && (*in != '\0')){
     for(j=i+1; j<=nlstate+ndeath; j++)      *alocc++ = *in++;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    }
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    if( *in == occ){
   } /* end i */      *(alocc)='\0';
       s=++in;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    }
     for(jj=1; jj<= nlstate+ndeath; jj++){   
       ps[ii][jj]=0;    if (s == t) {/* occ not found */
       ps[ii][ii]=1;      *(alocc-(in-s))='\0';
     }      in=s;
   }    }
     while ( *in != '\0'){
       *blocc++ = *in++;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);    *blocc='\0';
    }    return t;
     printf("\n ");  }
     }  char *cutv(char *blocc, char *alocc, char *in, char occ)
     printf("\n ");printf("%lf ",cov[2]);*/  {
 /*    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   goto end;*/       gives blocc="abcdef2ghi" and alocc="j".
     return ps;       If occ is not found blocc is null and alocc is equal to in. Returns alocc
 }    */
     char *s, *t;
 /**************** Product of 2 matrices ******************/    t=in;s=in;
     while (*in != '\0'){
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      while( *in == occ){
 {        *blocc++ = *in++;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        s=in;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      }
   /* in, b, out are matrice of pointers which should have been initialized      *blocc++ = *in++;
      before: only the contents of out is modified. The function returns    }
      a pointer to pointers identical to out */    if (s == t) /* occ not found */
   long i, j, k;      *(blocc-(in-s))='\0';
   for(i=nrl; i<= nrh; i++)    else
     for(k=ncolol; k<=ncoloh; k++)      *(blocc-(in-s)-1)='\0';
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    in=s;
         out[i][k] +=in[i][j]*b[j][k];    while ( *in != '\0'){
       *alocc++ = *in++;
   return out;    }
 }  
     *alocc='\0';
     return s;
 /************* Higher Matrix Product ***************/  }
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  int nbocc(char *s, char occ)
 {  {
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    int i,j=0;
      duration (i.e. until    int lg=20;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    i=0;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    lg=strlen(s);
      (typically every 2 years instead of every month which is too big).    for(i=0; i<= lg; i++) {
      Model is determined by parameters x and covariates have to be    if  (s[i] == occ ) j++;
      included manually here.    }
     return j;
      */  }
   
   int i, j, d, h, k;  /* void cutv(char *u,char *v, char*t, char occ) */
   double **out, cov[NCOVMAX];  /* { */
   double **newm;  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   /* Hstepm could be zero and should return the unit matrix */  /*      gives u="abcdef2ghi" and v="j" *\/ */
   for (i=1;i<=nlstate+ndeath;i++)  /*   int i,lg,j,p=0; */
     for (j=1;j<=nlstate+ndeath;j++){  /*   i=0; */
       oldm[i][j]=(i==j ? 1.0 : 0.0);  /*   lg=strlen(t); */
       po[i][j][0]=(i==j ? 1.0 : 0.0);  /*   for(j=0; j<=lg-1; j++) { */
     }  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  /*   } */
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){  /*   for(j=0; j<p; j++) { */
       newm=savm;  /*     (u[j] = t[j]); */
       /* Covariates have to be included here again */  /*   } */
       cov[1]=1.;  /*      u[p]='\0'; */
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /*    for(j=0; j<= lg; j++) { */
       for (k=1; k<=cptcovage;k++)  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*   } */
       for (k=1; k<=cptcovprod;k++)  /* } */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   /********************** nrerror ********************/
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  void nrerror(char error_text[])
       /*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,    fprintf(stderr,"ERREUR ...\n");
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    fprintf(stderr,"%s\n",error_text);
       savm=oldm;    exit(EXIT_FAILURE);
       oldm=newm;  }
     }  /*********************** vector *******************/
     for(i=1; i<=nlstate+ndeath; i++)  double *vector(int nl, int nh)
       for(j=1;j<=nlstate+ndeath;j++) {  {
         po[i][j][h]=newm[i][j];    double *v;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
          */    if (!v) nrerror("allocation failure in vector");
       }    return v-nl+NR_END;
   } /* end h */  }
   return po;  
 }  /************************ free vector ******************/
   void free_vector(double*v, int nl, int nh)
   {
 /*************** log-likelihood *************/    free((FREE_ARG)(v+nl-NR_END));
 double func( double *x)  }
 {  
   int i, ii, j, k, mi, d, kk;  /************************ivector *******************************/
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  int *ivector(long nl,long nh)
   double **out;  {
   double sw; /* Sum of weights */    int *v;
   double lli; /* Individual log likelihood */    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   long ipmx;    if (!v) nrerror("allocation failure in ivector");
   /*extern weight */    return v-nl+NR_END;
   /* We are differentiating ll according to initial status */  }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)  /******************free ivector **************************/
     printf(" %d\n",s[4][i]);  void free_ivector(int *v, long nl, long nh)
   */  {
   cov[1]=1.;    free((FREE_ARG)(v+nl-NR_END));
   }
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  /************************lvector *******************************/
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  long *lvector(long nl,long nh)
     for(mi=1; mi<= wav[i]-1; mi++){  {
       for (ii=1;ii<=nlstate+ndeath;ii++)    long *v;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       for(d=0; d<dh[mi][i]; d++){    if (!v) nrerror("allocation failure in ivector");
         newm=savm;    return v-nl+NR_END;
         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];  /******************free lvector **************************/
         }  void free_lvector(long *v, long nl, long nh)
          {
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    free((FREE_ARG)(v+nl-NR_END));
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  }
         savm=oldm;  
         oldm=newm;  /******************* imatrix *******************************/
          int **imatrix(long nrl, long nrh, long ncl, long nch) 
               /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       } /* end mult */  { 
          long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    int **m; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    
       ipmx +=1;    /* allocate pointers to rows */ 
       sw += weight[i];    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    if (!m) nrerror("allocation failure 1 in matrix()"); 
     } /* end of wave */    m += NR_END; 
   } /* end of individual */    m -= nrl; 
     
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    /* allocate rows and set pointers to them */ 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   return -l;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 }    m[nrl] += NR_END; 
     m[nrl] -= ncl; 
     
 /*********** Maximum Likelihood Estimation ***************/    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    /* return pointer to array of pointers to rows */ 
 {    return m; 
   int i,j, iter;  } 
   double **xi,*delti;  
   double fret;  /****************** free_imatrix *************************/
   xi=matrix(1,npar,1,npar);  void free_imatrix(m,nrl,nrh,ncl,nch)
   for (i=1;i<=npar;i++)        int **m;
     for (j=1;j<=npar;j++)        long nch,ncl,nrh,nrl; 
       xi[i][j]=(i==j ? 1.0 : 0.0);       /* free an int matrix allocated by imatrix() */ 
   printf("Powell\n");  { 
   powell(p,xi,npar,ftol,&iter,&fret,func);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  } 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  
   /******************* matrix *******************************/
 }  double **matrix(long nrl, long nrh, long ncl, long nch)
   {
 /**** Computes Hessian and covariance matrix ***/    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    double **m;
 {  
   double  **a,**y,*x,pd;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double **hess;    if (!m) nrerror("allocation failure 1 in matrix()");
   int i, j,jk;    m += NR_END;
   int *indx;    m -= nrl;
   
   double hessii(double p[], double delta, int theta, double delti[]);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double hessij(double p[], double delti[], int i, int j);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   void lubksb(double **a, int npar, int *indx, double b[]) ;    m[nrl] += NR_END;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    m[nrl] -= ncl;
   
   hess=matrix(1,npar,1,npar);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
   printf("\nCalculation of the hessian matrix. Wait...\n");    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   for (i=1;i<=npar;i++){  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
     printf("%d",i);fflush(stdout);  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     hess[i][i]=hessii(p,ftolhess,i,delti);     */
     /*printf(" %f ",p[i]);*/  }
     /*printf(" %lf ",hess[i][i]);*/  
   }  /*************************free matrix ************************/
    void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   for (i=1;i<=npar;i++) {  {
     for (j=1;j<=npar;j++)  {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       if (j>i) {    free((FREE_ARG)(m+nrl-NR_END));
         printf(".%d%d",i,j);fflush(stdout);  }
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];      /******************* ma3x *******************************/
         /*printf(" %lf ",hess[i][j]);*/  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       }  {
     }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   }    double ***m;
   printf("\n");  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    if (!m) nrerror("allocation failure 1 in matrix()");
      m += NR_END;
   a=matrix(1,npar,1,npar);    m -= nrl;
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   indx=ivector(1,npar);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for (i=1;i<=npar;i++)    m[nrl] += NR_END;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    m[nrl] -= ncl;
   ludcmp(a,npar,indx,&pd);  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     x[j]=1;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     lubksb(a,npar,indx,x);    m[nrl][ncl] += NR_END;
     for (i=1;i<=npar;i++){    m[nrl][ncl] -= nll;
       matcov[i][j]=x[i];    for (j=ncl+1; j<=nch; j++) 
     }      m[nrl][j]=m[nrl][j-1]+nlay;
   }    
     for (i=nrl+1; i<=nrh; i++) {
   printf("\n#Hessian matrix#\n");      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   for (i=1;i<=npar;i++) {      for (j=ncl+1; j<=nch; j++) 
     for (j=1;j<=npar;j++) {        m[i][j]=m[i][j-1]+nlay;
       printf("%.3e ",hess[i][j]);    }
     }    return m; 
     printf("\n");    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     */
   /* Recompute Inverse */  }
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  /*************************free ma3x ************************/
   ludcmp(a,npar,indx,&pd);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
   /*  printf("\n#Hessian matrix recomputed#\n");    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for (j=1;j<=npar;j++) {    free((FREE_ARG)(m+nrl-NR_END));
     for (i=1;i<=npar;i++) x[i]=0;  }
     x[j]=1;  
     lubksb(a,npar,indx,x);  /*************** function subdirf ***********/
     for (i=1;i<=npar;i++){  char *subdirf(char fileres[])
       y[i][j]=x[i];  {
       printf("%.3e ",y[i][j]);    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
     printf("\n");    strcat(tmpout,"/"); /* Add to the right */
   }    strcat(tmpout,fileres);
   */    return tmpout;
   }
   free_matrix(a,1,npar,1,npar);  
   free_matrix(y,1,npar,1,npar);  /*************** function subdirf2 ***********/
   free_vector(x,1,npar);  char *subdirf2(char fileres[], char *preop)
   free_ivector(indx,1,npar);  {
   free_matrix(hess,1,npar,1,npar);    
     /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
 }    strcat(tmpout,"/");
     strcat(tmpout,preop);
 /*************** hessian matrix ****************/    strcat(tmpout,fileres);
 double hessii( double x[], double delta, int theta, double delti[])    return tmpout;
 {  }
   int i;  
   int l=1, lmax=20;  /*************** function subdirf3 ***********/
   double k1,k2;  char *subdirf3(char fileres[], char *preop, char *preop2)
   double p2[NPARMAX+1];  {
   double res;    
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    /* Caution optionfilefiname is hidden */
   double fx;    strcpy(tmpout,optionfilefiname);
   int k=0,kmax=10;    strcat(tmpout,"/");
   double l1;    strcat(tmpout,preop);
     strcat(tmpout,preop2);
   fx=func(x);    strcat(tmpout,fileres);
   for (i=1;i<=npar;i++) p2[i]=x[i];    return tmpout;
   for(l=0 ; l <=lmax; l++){  }
     l1=pow(10,l);  
     delts=delt;  /***************** f1dim *************************/
     for(k=1 ; k <kmax; k=k+1){  extern int ncom; 
       delt = delta*(l1*k);  extern double *pcom,*xicom;
       p2[theta]=x[theta] +delt;  extern double (*nrfunc)(double []); 
       k1=func(p2)-fx;   
       p2[theta]=x[theta]-delt;  double f1dim(double x) 
       k2=func(p2)-fx;  { 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    int j; 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    double f;
          double *xt; 
 #ifdef DEBUG   
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    xt=vector(1,ncom); 
 #endif    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    f=(*nrfunc)(xt); 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    free_vector(xt,1,ncom); 
         k=kmax;    return f; 
       }  } 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  
         k=kmax; l=lmax*10.;  /*****************brent *************************/
       }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  { 
         delts=delt;    int iter; 
       }    double a,b,d,etemp;
     }    double fu,fv,fw,fx;
   }    double ftemp;
   delti[theta]=delts;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   return res;    double e=0.0; 
     
 }    a=(ax < cx ? ax : cx); 
     b=(ax > cx ? ax : cx); 
 double hessij( double x[], double delti[], int thetai,int thetaj)    x=w=v=bx; 
 {    fw=fv=fx=(*f)(x); 
   int i;    for (iter=1;iter<=ITMAX;iter++) { 
   int l=1, l1, lmax=20;      xm=0.5*(a+b); 
   double k1,k2,k3,k4,res,fx;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   double p2[NPARMAX+1];      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   int k;      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
   fx=func(x);  #ifdef DEBUG
   for (k=1; k<=2; k++) {      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);
     p2[thetai]=x[thetai]+delti[thetai]/k;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  #endif
     k1=func(p2)-fx;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
          *xmin=x; 
     p2[thetai]=x[thetai]+delti[thetai]/k;        return fx; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      } 
     k2=func(p2)-fx;      ftemp=fu;
        if (fabs(e) > tol1) { 
     p2[thetai]=x[thetai]-delti[thetai]/k;        r=(x-w)*(fx-fv); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        q=(x-v)*(fx-fw); 
     k3=func(p2)-fx;        p=(x-v)*q-(x-w)*r; 
          q=2.0*(q-r); 
     p2[thetai]=x[thetai]-delti[thetai]/k;        if (q > 0.0) p = -p; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        q=fabs(q); 
     k4=func(p2)-fx;        etemp=e; 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        e=d; 
 #ifdef DEBUG        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     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);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 #endif        else { 
   }          d=p/q; 
   return res;          u=x+d; 
 }          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
 /************** Inverse of matrix **************/        } 
 void ludcmp(double **a, int n, int *indx, double *d)      } else { 
 {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   int i,imax,j,k;      } 
   double big,dum,sum,temp;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double *vv;      fu=(*f)(u); 
        if (fu <= fx) { 
   vv=vector(1,n);        if (u >= x) a=x; else b=x; 
   *d=1.0;        SHFT(v,w,x,u) 
   for (i=1;i<=n;i++) {          SHFT(fv,fw,fx,fu) 
     big=0.0;          } else { 
     for (j=1;j<=n;j++)            if (u < x) a=u; else b=u; 
       if ((temp=fabs(a[i][j])) > big) big=temp;            if (fu <= fw || w == x) { 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");              v=w; 
     vv[i]=1.0/big;              w=u; 
   }              fv=fw; 
   for (j=1;j<=n;j++) {              fw=fu; 
     for (i=1;i<j;i++) {            } else if (fu <= fv || v == x || v == w) { 
       sum=a[i][j];              v=u; 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];              fv=fu; 
       a[i][j]=sum;            } 
     }          } 
     big=0.0;    } 
     for (i=j;i<=n;i++) {    nrerror("Too many iterations in brent"); 
       sum=a[i][j];    *xmin=x; 
       for (k=1;k<j;k++)    return fx; 
         sum -= a[i][k]*a[k][j];  } 
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {  /****************** mnbrak ***********************/
         big=dum;  
         imax=i;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       }              double (*func)(double)) 
     }  { 
     if (j != imax) {    double ulim,u,r,q, dum;
       for (k=1;k<=n;k++) {    double fu; 
         dum=a[imax][k];   
         a[imax][k]=a[j][k];    *fa=(*func)(*ax); 
         a[j][k]=dum;    *fb=(*func)(*bx); 
       }    if (*fb > *fa) { 
       *d = -(*d);      SHFT(dum,*ax,*bx,dum) 
       vv[imax]=vv[j];        SHFT(dum,*fb,*fa,dum) 
     }        } 
     indx[j]=imax;    *cx=(*bx)+GOLD*(*bx-*ax); 
     if (a[j][j] == 0.0) a[j][j]=TINY;    *fc=(*func)(*cx); 
     if (j != n) {    while (*fb > *fc) { 
       dum=1.0/(a[j][j]);      r=(*bx-*ax)*(*fb-*fc); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      q=(*bx-*cx)*(*fb-*fa); 
     }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   free_vector(vv,1,n);  /* Doesn't work */      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 ;      if ((*bx-u)*(u-*cx) > 0.0) { 
 }        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
 void lubksb(double **a, int n, int *indx, double b[])        fu=(*func)(u); 
 {        if (fu < *fc) { 
   int i,ii=0,ip,j;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double sum;            SHFT(*fb,*fc,fu,(*func)(u)) 
              } 
   for (i=1;i<=n;i++) {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     ip=indx[i];        u=ulim; 
     sum=b[ip];        fu=(*func)(u); 
     b[ip]=b[i];      } else { 
     if (ii)        u=(*cx)+GOLD*(*cx-*bx); 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        fu=(*func)(u); 
     else if (sum) ii=i;      } 
     b[i]=sum;      SHFT(*ax,*bx,*cx,u) 
   }        SHFT(*fa,*fb,*fc,fu) 
   for (i=n;i>=1;i--) {        } 
     sum=b[i];  } 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];  /*************** linmin ************************/
   }  
 }  int ncom; 
   double *pcom,*xicom;
 /************ Frequencies ********************/  double (*nrfunc)(double []); 
 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)   
 {  /* Some frequencies */  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
    { 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    double brent(double ax, double bx, double cx, 
   double ***freq; /* Frequencies */                 double (*f)(double), double tol, double *xmin); 
   double *pp;    double f1dim(double x); 
   double pos, k2, dateintsum=0,k2cpt=0;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   FILE *ficresp;                double *fc, double (*func)(double)); 
   char fileresp[FILENAMELENGTH];    int j; 
      double xx,xmin,bx,ax; 
   pp=vector(1,nlstate);    double fx,fb,fa;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);   
   strcpy(fileresp,"p");    ncom=n; 
   strcat(fileresp,fileres);    pcom=vector(1,n); 
   if((ficresp=fopen(fileresp,"w"))==NULL) {    xicom=vector(1,n); 
     printf("Problem with prevalence resultfile: %s\n", fileresp);    nrfunc=func; 
     exit(0);    for (j=1;j<=n;j++) { 
   }      pcom[j]=p[j]; 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      xicom[j]=xi[j]; 
   j1=0;    } 
      ax=0.0; 
   j=cptcoveff;    xx=1.0; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
      *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   for(k1=1; k1<=j;k1++){  #ifdef DEBUG
     for(i1=1; i1<=ncodemax[k1];i1++){    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       j1++;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  #endif
         scanf("%d", i);*/    for (j=1;j<=n;j++) { 
       for (i=-1; i<=nlstate+ndeath; i++)        xi[j] *= xmin; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)        p[j] += xi[j]; 
           for(m=agemin; m <= agemax+3; m++)    } 
             freq[i][jk][m]=0;    free_vector(xicom,1,n); 
          free_vector(pcom,1,n); 
       dateintsum=0;  } 
       k2cpt=0;  
       for (i=1; i<=imx; i++) {  char *asc_diff_time(long time_sec, char ascdiff[])
         bool=1;  {
         if  (cptcovn>0) {    long sec_left, days, hours, minutes;
           for (z1=1; z1<=cptcoveff; z1++)    days = (time_sec) / (60*60*24);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    sec_left = (time_sec) % (60*60*24);
               bool=0;    hours = (sec_left) / (60*60) ;
         }    sec_left = (sec_left) %(60*60);
         if (bool==1) {    minutes = (sec_left) /60;
           for(m=firstpass; m<=lastpass; m++){    sec_left = (sec_left) % (60);
             k2=anint[m][i]+(mint[m][i]/12.);    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    return ascdiff;
               if(agev[m][i]==0) agev[m][i]=agemax+1;  }
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {  /*************** powell ************************/
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];              double (*func)(double [])) 
               }  { 
                  void linmin(double p[], double xi[], int n, double *fret, 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {                double (*func)(double [])); 
                 dateintsum=dateintsum+k2;    int i,ibig,j; 
                 k2cpt++;    double del,t,*pt,*ptt,*xit;
               }    double fp,fptt;
             }    double *xits;
           }    int niterf, itmp;
         }  
       }    pt=vector(1,n); 
            ptt=vector(1,n); 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    xit=vector(1,n); 
     xits=vector(1,n); 
       if  (cptcovn>0) {    *fret=(*func)(p); 
         fprintf(ficresp, "\n#********** Variable ");    for (j=1;j<=n;j++) pt[j]=p[j]; 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for (*iter=1;;++(*iter)) { 
         fprintf(ficresp, "**********\n#");      fp=(*fret); 
       }      ibig=0; 
       for(i=1; i<=nlstate;i++)      del=0.0; 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      last_time=curr_time;
       fprintf(ficresp, "\n");      (void) gettimeofday(&curr_time,&tzp);
            printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
       for(i=(int)agemin; i <= (int)agemax+3; i++){      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
         if(i==(int)agemax+3)  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
           printf("Total");     for (i=1;i<=n;i++) {
         else        printf(" %d %.12f",i, p[i]);
           printf("Age %d", i);        fprintf(ficlog," %d %.12lf",i, p[i]);
         for(jk=1; jk <=nlstate ; jk++){        fprintf(ficrespow," %.12lf", p[i]);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      }
             pp[jk] += freq[jk][m][i];      printf("\n");
         }      fprintf(ficlog,"\n");
         for(jk=1; jk <=nlstate ; jk++){      fprintf(ficrespow,"\n");fflush(ficrespow);
           for(m=-1, pos=0; m <=0 ; m++)      if(*iter <=3){
             pos += freq[jk][m][i];        tm = *localtime(&curr_time.tv_sec);
           if(pp[jk]>=1.e-10)        strcpy(strcurr,asctime(&tm));
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  /*       asctime_r(&tm,strcurr); */
           else        forecast_time=curr_time; 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        itmp = strlen(strcurr);
         }        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           strcurr[itmp-1]='\0';
         for(jk=1; jk <=nlstate ; jk++){        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
             pp[jk] += freq[jk][m][i];        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);
         for(jk=1,pos=0; jk <=nlstate ; jk++)  /*      asctime_r(&tmf,strfor); */
           pos += pp[jk];          strcpy(strfor,asctime(&tmf));
         for(jk=1; jk <=nlstate ; jk++){          itmp = strlen(strfor);
           if(pos>=1.e-5)          if(strfor[itmp-1]=='\n')
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          strfor[itmp-1]='\0';
           else          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);
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
           if( i <= (int) agemax){        }
             if(pos>=1.e-5){      }
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      for (i=1;i<=n;i++) { 
               probs[i][jk][j1]= pp[jk]/pos;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        fptt=(*fret); 
             }  #ifdef DEBUG
             else        printf("fret=%lf \n",*fret);
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        fprintf(ficlog,"fret=%lf \n",*fret);
           }  #endif
         }        printf("%d",i);fflush(stdout);
                fprintf(ficlog,"%d",i);fflush(ficlog);
         for(jk=-1; jk <=nlstate+ndeath; jk++)        linmin(p,xit,n,fret,func); 
           for(m=-1; m <=nlstate+ndeath; m++)        if (fabs(fptt-(*fret)) > del) { 
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          del=fabs(fptt-(*fret)); 
         if(i <= (int) agemax)          ibig=i; 
           fprintf(ficresp,"\n");        } 
         printf("\n");  #ifdef DEBUG
       }        printf("%d %.12e",i,(*fret));
     }        fprintf(ficlog,"%d %.12e",i,(*fret));
   }        for (j=1;j<=n;j++) {
   dateintmean=dateintsum/k2cpt;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
            printf(" x(%d)=%.12e",j,xit[j]);
   fclose(ficresp);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        }
   free_vector(pp,1,nlstate);        for(j=1;j<=n;j++) {
            printf(" p=%.12e",p[j]);
   /* End of Freq */          fprintf(ficlog," p=%.12e",p[j]);
 }        }
         printf("\n");
 /************ Prevalence ********************/        fprintf(ficlog,"\n");
 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)  #endif
 {  /* Some frequencies */      } 
        if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  #ifdef DEBUG
   double ***freq; /* Frequencies */        int k[2],l;
   double *pp;        k[0]=1;
   double pos, k2;        k[1]=-1;
         printf("Max: %.12e",(*func)(p));
   pp=vector(1,nlstate);        fprintf(ficlog,"Max: %.12e",(*func)(p));
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        for (j=1;j<=n;j++) {
            printf(" %.12e",p[j]);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          fprintf(ficlog," %.12e",p[j]);
   j1=0;        }
          printf("\n");
   j=cptcoveff;        fprintf(ficlog,"\n");
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        for(l=0;l<=1;l++) {
            for (j=1;j<=n;j++) {
  for(k1=1; k1<=j;k1++){            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     for(i1=1; i1<=ncodemax[k1];i1++){            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       j1++;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
            }
       for (i=-1; i<=nlstate+ndeath; i++)            printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         for (jk=-1; jk<=nlstate+ndeath; jk++)            fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           for(m=agemin; m <= agemax+3; m++)        }
             freq[i][jk][m]=0;  #endif
        
       for (i=1; i<=imx; i++) {  
         bool=1;        free_vector(xit,1,n); 
         if  (cptcovn>0) {        free_vector(xits,1,n); 
           for (z1=1; z1<=cptcoveff; z1++)        free_vector(ptt,1,n); 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        free_vector(pt,1,n); 
               bool=0;        return; 
         }      } 
         if (bool==1) {      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
           for(m=firstpass; m<=lastpass; m++){      for (j=1;j<=n;j++) { 
             k2=anint[m][i]+(mint[m][i]/12.);        ptt[j]=2.0*p[j]-pt[j]; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        xit[j]=p[j]-pt[j]; 
               if(agev[m][i]==0) agev[m][i]=agemax+1;        pt[j]=p[j]; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;      } 
               if (m<lastpass)      fptt=(*func)(ptt); 
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      if (fptt < fp) { 
               else        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        if (t < 0.0) { 
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          linmin(p,xit,n,fret,func); 
             }          for (j=1;j<=n;j++) { 
           }            xi[j][ibig]=xi[j][n]; 
         }            xi[j][n]=xit[j]; 
       }          }
         for(i=(int)agemin; i <= (int)agemax+3; i++){  #ifdef DEBUG
           for(jk=1; jk <=nlstate ; jk++){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
               pp[jk] += freq[jk][m][i];          for(j=1;j<=n;j++){
           }            printf(" %.12e",xit[j]);
           for(jk=1; jk <=nlstate ; jk++){            fprintf(ficlog," %.12e",xit[j]);
             for(m=-1, pos=0; m <=0 ; m++)          }
             pos += freq[jk][m][i];          printf("\n");
         }          fprintf(ficlog,"\n");
          #endif
          for(jk=1; jk <=nlstate ; jk++){        }
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      } 
              pp[jk] += freq[jk][m][i];    } 
          }  } 
            
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  /**** Prevalence limit (stable or period prevalence)  ****************/
   
          for(jk=1; jk <=nlstate ; jk++){            double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
            if( i <= (int) agemax){  {
              if(pos>=1.e-5){    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
                probs[i][jk][j1]= pp[jk]/pos;       matrix by transitions matrix until convergence is reached */
              }  
            }    int i, ii,j,k;
          }    double min, max, maxmin, maxmax,sumnew=0.;
              /* double **matprod2(); */ /* test */
         }    double **out, cov[NCOVMAX+1], **pmij();
     }    double **newm;
   }    double agefin, delaymax=50 ; /* Max number of years to converge */
   
      for (ii=1;ii<=nlstate+ndeath;ii++)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for (j=1;j<=nlstate+ndeath;j++){
   free_vector(pp,1,nlstate);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        }
 }  /* End of Freq */  
      cov[1]=1.;
 /************* Waves Concatenation ***************/   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 {      newm=savm;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      /* Covariates have to be included here again */
      Death is a valid wave (if date is known).      cov[2]=agefin;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      for (k=1; k<=cptcovn;k++) {
      and mw[mi+1][i]. dh depends on stepm.        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]]);*/
       }
   int i, mi, m;      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
      double sum=0., jmean=0.;*/      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
       
   int j, k=0,jk, ju, jl;      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   double sum=0.;      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   jmin=1e+5;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   jmax=-1;      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   jmean=0.;      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
   for(i=1; i<=imx; i++){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
     mi=0;      
     m=firstpass;      savm=oldm;
     while(s[m][i] <= nlstate){      oldm=newm;
       if(s[m][i]>=1)      maxmax=0.;
         mw[++mi][i]=m;      for(j=1;j<=nlstate;j++){
       if(m >=lastpass)        min=1.;
         break;        max=0.;
       else        for(i=1; i<=nlstate; i++) {
         m++;          sumnew=0;
     }/* end while */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     if (s[m][i] > nlstate){          prlim[i][j]= newm[i][j]/(1-sumnew);
       mi++;     /* Death is another wave */          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
       /* if(mi==0)  never been interviewed correctly before death */          max=FMAX(max,prlim[i][j]);
          /* Only death is a correct wave */          min=FMIN(min,prlim[i][j]);
       mw[mi][i]=m;        }
     }        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
     wav[i]=mi;      }
     if(mi==0)      if(maxmax < ftolpl){
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        return prlim;
   }      }
     }
   for(i=1; i<=imx; i++){  }
     for(mi=1; mi<wav[i];mi++){  
       if (stepm <=0)  /*************** transition probabilities ***************/ 
         dh[mi][i]=1;  
       else{  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         if (s[mw[mi+1][i]][i] > nlstate) {  {
           if (agedc[i] < 2*AGESUP) {    /* According to parameters values stored in x and the covariate's values stored in cov,
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);       computes the probability to be observed in state j being in state i by appying the
           if(j==0) j=1;  /* Survives at least one month after exam */       model to the ncovmodel covariates (including constant and age).
           k=k+1;       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
           if (j >= jmax) jmax=j;       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
           if (j <= jmin) jmin=j;       ncth covariate in the global vector x is given by the formula:
           sum=sum+j;       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
           /*if (j<0) printf("j=%d num=%d \n",j,i); */       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
           }       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
         }       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
         else{       Outputs ps[i][j] the probability to be observed in j being in j according to
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
           k=k+1;    */
           if (j >= jmax) jmax=j;    double s1, lnpijopii;
           else if (j <= jmin)jmin=j;    /*double t34;*/
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    int i,j,j1, nc, ii, jj;
           sum=sum+j;  
         }      for(i=1; i<= nlstate; i++){
         jk= j/stepm;        for(j=1; j<i;j++){
         jl= j -jk*stepm;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         ju= j -(jk+1)*stepm;            /*lnpijopii += param[i][j][nc]*cov[nc];*/
         if(jl <= -ju)            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
           dh[mi][i]=jk;  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         else          }
           dh[mi][i]=jk+1;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         if(dh[mi][i]==0)  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
           dh[mi][i]=1; /* At least one step */        }
       }        for(j=i+1; j<=nlstate+ndeath;j++){
     }          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   }            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
   jmean=sum/k;            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
  }          }
 /*********** Tricode ****************************/          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
 void tricode(int *Tvar, int **nbcode, int imx)        }
 {      }
   int Ndum[20],ij=1, k, j, i;      
   int cptcode=0;      for(i=1; i<= nlstate; i++){
   cptcoveff=0;        s1=0;
          for(j=1; j<i; j++){
   for (k=0; k<19; k++) Ndum[k]=0;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   for (k=1; k<=7; k++) ncodemax[k]=0;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        for(j=i+1; j<=nlstate+ndeath; j++){
     for (i=1; i<=imx; i++) {          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       ij=(int)(covar[Tvar[j]][i]);          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       Ndum[ij]++;        }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       if (ij > cptcode) cptcode=ij;        ps[i][i]=1./(s1+1.);
     }        /* Computing other pijs */
         for(j=1; j<i; j++)
     for (i=0; i<=cptcode; i++) {          ps[i][j]= exp(ps[i][j])*ps[i][i];
       if(Ndum[i]!=0) ncodemax[j]++;        for(j=i+1; j<=nlstate+ndeath; j++)
     }          ps[i][j]= exp(ps[i][j])*ps[i][i];
     ij=1;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       } /* end i */
       
     for (i=1; i<=ncodemax[j]; i++) {      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for (k=0; k<=19; k++) {        for(jj=1; jj<= nlstate+ndeath; jj++){
         if (Ndum[k] != 0) {          ps[ii][jj]=0;
           nbcode[Tvar[j]][ij]=k;          ps[ii][ii]=1;
                  }
           ij++;      }
         }      
         if (ij > ncodemax[j]) break;      
       }        /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
     }      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   }        /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       /*   } */
  for (k=0; k<19; k++) Ndum[k]=0;      /*   printf("\n "); */
       /* } */
  for (i=1; i<=ncovmodel-2; i++) {      /* printf("\n ");printf("%lf ",cov[2]);*/
       ij=Tvar[i];      /*
       Ndum[ij]++;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
     }        goto end;*/
       return ps;
  ij=1;  }
  for (i=1; i<=10; i++) {  
    if((Ndum[i]!=0) && (i<=ncovcol)){  /**************** Product of 2 matrices ******************/
      Tvaraff[ij]=i;  
      ij++;  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
    }  {
  }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     cptcoveff=ij-1;    /* in, b, out are matrice of pointers which should have been initialized 
 }       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
 /*********** Health Expectancies ****************/    int i, j, k;
     for(i=nrl; i<= nrh; i++)
 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 )      for(k=ncolol; k<=ncoloh; k++){
         out[i][k]=0.;
 {        for(j=ncl; j<=nch; j++)
   /* Health expectancies */          out[i][k] +=in[i][j]*b[j][k];
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;      }
   double age, agelim, hf;    return out;
   double ***p3mat,***varhe;  }
   double **dnewm,**doldm;  
   double *xp;  
   double **gp, **gm;  /************* Higher Matrix Product ***************/
   double ***gradg, ***trgradg;  
   int theta;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    /* Computes the transition matrix starting at age 'age' over 
   xp=vector(1,npar);       'nhstepm*hstepm*stepm' months (i.e. until
   dnewm=matrix(1,nlstate*2,1,npar);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   doldm=matrix(1,nlstate*2,1,nlstate*2);       nhstepm*hstepm matrices. 
         Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   fprintf(ficreseij,"# Health expectancies\n");       (typically every 2 years instead of every month which is too big 
   fprintf(ficreseij,"# Age");       for the memory).
   for(i=1; i<=nlstate;i++)       Model is determined by parameters x and covariates have to be 
     for(j=1; j<=nlstate;j++)       included manually here. 
       fprintf(ficreseij," %1d-%1d (SE)",i,j);  
   fprintf(ficreseij,"\n");       */
   
   if(estepm < stepm){    int i, j, d, h, k;
     printf ("Problem %d lower than %d\n",estepm, stepm);    double **out, cov[NCOVMAX+1];
   }    double **newm;
   else  hstepm=estepm;    
   /* We compute the life expectancy from trapezoids spaced every estepm months    /* Hstepm could be zero and should return the unit matrix */
    * This is mainly to measure the difference between two models: for example    for (i=1;i<=nlstate+ndeath;i++)
    * if stepm=24 months pijx are given only every 2 years and by summing them      for (j=1;j<=nlstate+ndeath;j++){
    * we are calculating an estimate of the Life Expectancy assuming a linear        oldm[i][j]=(i==j ? 1.0 : 0.0);
    * progression inbetween and thus overestimating or underestimating according        po[i][j][0]=(i==j ? 1.0 : 0.0);
    * 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    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
    * to compare the new estimate of Life expectancy with the same linear    for(h=1; h <=nhstepm; h++){
    * hypothesis. A more precise result, taking into account a more precise      for(d=1; d <=hstepm; d++){
    * curvature will be obtained if estepm is as small as stepm. */        newm=savm;
         /* Covariates have to be included here again */
   /* For example we decided to compute the life expectancy with the smallest unit */        cov[1]=1.;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
      nhstepm is the number of hstepm from age to agelim        for (k=1; k<=cptcovn;k++) 
      nstepm is the number of stepm from age to agelin.          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
      Look at hpijx to understand the reason of that which relies in memory size        for (k=1; k<=cptcovage;k++)
      and note for a fixed period like estepm months */          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
      survival function given by stepm (the optimization length). Unfortunately it          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      means that if the survival funtion is printed only each two years of age and if  
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  
      results. So we changed our mind and took the option of the best precision.        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   */        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
   agelim=AGESUP;        savm=oldm;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        oldm=newm;
     /* nhstepm age range expressed in number of stepm */      }
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      for(i=1; i<=nlstate+ndeath; i++)
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */        for(j=1;j<=nlstate+ndeath;j++) {
     /* if (stepm >= YEARM) hstepm=1;*/          po[i][j][h]=newm[i][j];
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);      /*printf("h=%d ",h);*/
     gp=matrix(0,nhstepm,1,nlstate*2);    } /* end h */
     gm=matrix(0,nhstepm,1,nlstate*2);  /*     printf("\n H=%d \n",h); */
     return po;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    
    /*************** log-likelihood *************/
   double func( double *x)
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  {
     int i, ii, j, k, mi, d, kk;
     /* Computing Variances of health expectancies */    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     double **out;
      for(theta=1; theta <=npar; theta++){    double sw; /* Sum of weights */
       for(i=1; i<=npar; i++){    double lli; /* Individual log likelihood */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int s1, s2;
       }    double bbh, survp;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      long ipmx;
      /*extern weight */
       cptj=0;    /* We are differentiating ll according to initial status */
       for(j=1; j<= nlstate; j++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         for(i=1; i<=nlstate; i++){    /*for(i=1;i<imx;i++) 
           cptj=cptj+1;      printf(" %d\n",s[4][i]);
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    */
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    cov[1]=1.;
           }  
         }    for(k=1; k<=nlstate; k++) ll[k]=0.;
       }  
          if(mle==1){
            for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(i=1; i<=npar; i++)        /* Computes the values of the ncovmodel covariates of the model
         xp[i] = x[i] - (i==theta ?delti[theta]:0);           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);             Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
                 to be observed in j being in i according to the model.
       cptj=0;         */
       for(j=1; j<= nlstate; j++){        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
         for(i=1;i<=nlstate;i++){          cov[2+k]=covar[Tvar[k]][i];
           cptj=cptj+1;        }
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
           }           has been calculated etc */
         }        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (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*2; j++)            }
         for(h=0; h<=nhstepm-1; 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;
             for (kk=1; kk<=cptcovage;kk++) {
      }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
                }
 /* End theta */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);            savm=oldm;
             oldm=newm;
      for(h=0; h<=nhstepm-1; h++)          } /* end mult */
       for(j=1; j<=nlstate*2;j++)        
         for(theta=1; theta <=npar; theta++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         trgradg[h][j][theta]=gradg[h][theta][j];          /* 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 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
      for(i=1;i<=nlstate*2;i++)           * the nearest (and in case of equal distance, to the lowest) interval but now
       for(j=1;j<=nlstate*2;j++)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         varhe[i][j][(int)age] =0.;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
     for(h=0;h<=nhstepm-1;h++){           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       for(k=0;k<=nhstepm-1;k++){           * -stepm/2 to stepm/2 .
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);           * For stepm=1 the results are the same as for previous versions of Imach.
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);           * For stepm > 1 the results are less biased than in previous versions. 
         for(i=1;i<=nlstate*2;i++)           */
           for(j=1;j<=nlstate*2;j++)          s1=s[mw[mi][i]][i];
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          s2=s[mw[mi+1][i]][i];
       }          bbh=(double)bh[mi][i]/(double)stepm; 
     }          /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
                 */
     /* Computing expectancies */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     for(i=1; i<=nlstate;i++)          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 (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){               then the contribution to the likelihood is the probability to 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;               die between last step unit time and current  step unit time, 
                         which is also equal to probability to die before dh 
 /* 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]);*/               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
     fprintf(ficreseij,"%3.0f",age );          and not the date of a change in health state. The former idea was
     cptj=0;          to consider that at each interview the state was recorded
     for(i=1; i<=nlstate;i++)          (healthy, disable or death) and IMaCh was corrected; but when we
       for(j=1; j<=nlstate;j++){          introduced the exact date of death then we should have modified
         cptj++;          the contribution of an exact death to the likelihood. This new
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          contribution is smaller and very dependent of the step unit
       }          stepm. It is no more the probability to die between last interview
     fprintf(ficreseij,"\n");          and month of death but the probability to survive from last
              interview up to one month before death multiplied by the
     free_matrix(gm,0,nhstepm,1,nlstate*2);          probability to die within a month. Thanks to Chris
     free_matrix(gp,0,nhstepm,1,nlstate*2);          Jackson for correcting this bug.  Former versions increased
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);          mortality artificially. The bad side is that we add another loop
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          which slows down the processing. The difference can be up to 10%
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          lower mortality.
   }            */
   free_vector(xp,1,npar);            lli=log(out[s1][s2] - savm[s1][s2]);
   free_matrix(dnewm,1,nlstate*2,1,npar);  
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          } else if  (s2==-2) {
 }            for (j=1,survp=0. ; j<=nlstate; j++) 
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 /************ Variance ******************/            /*survp += out[s1][j]; */
 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)            lli= log(survp);
 {          }
   /* Variance of health expectancies */          
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          else if  (s2==-4) { 
   double **newm;            for (j=3,survp=0. ; j<=nlstate; j++)  
   double **dnewm,**doldm;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   int i, j, nhstepm, hstepm, h, nstepm ;            lli= log(survp); 
   int k, cptcode;          } 
   double *xp;  
   double **gp, **gm;          else if  (s2==-5) { 
   double ***gradg, ***trgradg;            for (j=1,survp=0. ; j<=2; j++)  
   double ***p3mat;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double age,agelim, hf;            lli= log(survp); 
   int theta;          } 
           
    fprintf(ficresvij,"# Covariances of life expectancies\n");          else{
   fprintf(ficresvij,"# Age");            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   for(i=1; i<=nlstate;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 */
     for(j=1; j<=nlstate;j++)          } 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   fprintf(ficresvij,"\n");          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   xp=vector(1,npar);          ipmx +=1;
   dnewm=matrix(1,nlstate,1,npar);          sw += weight[i];
   doldm=matrix(1,nlstate,1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
   if(estepm < stepm){      } /* end of individual */
     printf ("Problem %d lower than %d\n",estepm, stepm);    }  else if(mle==2){
   }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   else  hstepm=estepm;          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   /* For example we decided to compute the life expectancy with the smallest unit */        for(mi=1; mi<= wav[i]-1; mi++){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          for (ii=1;ii<=nlstate+ndeath;ii++)
      nhstepm is the number of hstepm from age to agelim            for (j=1;j<=nlstate+ndeath;j++){
      nstepm is the number of stepm from age to agelin.              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      Look at hpijx to understand the reason of that which relies in memory size              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      and note for a fixed period like k years */            }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          for(d=0; d<=dh[mi][i]; d++){
      survival function given by stepm (the optimization length). Unfortunately it            newm=savm;
      means that if the survival funtion is printed only each two years of age and if            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            for (kk=1; kk<=cptcovage;kk++) {
      results. So we changed our mind and took the option of the best precision.              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   */            }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   agelim = AGESUP;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            savm=oldm;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            oldm=newm;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          } /* end mult */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          s1=s[mw[mi][i]][i];
     gp=matrix(0,nhstepm,1,nlstate);          s2=s[mw[mi+1][i]][i];
     gm=matrix(0,nhstepm,1,nlstate);          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     for(theta=1; theta <=npar; theta++){          ipmx +=1;
       for(i=1; i<=npar; i++){ /* Computes gradient */          sw += weight[i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }        } /* end of wave */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        } /* end of individual */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       if (popbased==1) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(i=1; i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
           prlim[i][i]=probs[(int)age][i][ij];          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<= nlstate; j++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(h=0; h<=nhstepm; h++){            }
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          for(d=0; d<dh[mi][i]; d++){
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(i=1; i<=npar; i++) /* Computes gradient */            }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            savm=oldm;
              oldm=newm;
       if (popbased==1) {          } /* end mult */
         for(i=1; i<=nlstate;i++)        
           prlim[i][i]=probs[(int)age][i][ij];          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
       for(j=1; j<= nlstate; j++){          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         for(h=0; h<=nhstepm; h++){          ipmx +=1;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          sw += weight[i];
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }        } /* end of wave */
       }      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
       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];
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
     } /* End theta */            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     for(h=0; h<=nhstepm; h++)          for(d=0; d<dh[mi][i]; d++){
       for(j=1; j<=nlstate;j++)            newm=savm;
         for(theta=1; theta <=npar; theta++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           trgradg[h][j][theta]=gradg[h][theta][j];            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            }
     for(i=1;i<=nlstate;i++)          
       for(j=1;j<=nlstate;j++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         vareij[i][j][(int)age] =0.;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     for(h=0;h<=nhstepm;h++){            oldm=newm;
       for(k=0;k<=nhstepm;k++){          } /* end mult */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          s1=s[mw[mi][i]][i];
         for(i=1;i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
           for(j=1;j<=nlstate;j++)          if( s2 > nlstate){ 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;            lli=log(out[s1][s2] - savm[s1][s2]);
       }          }else{
     }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
     fprintf(ficresvij,"%.0f ",age );          ipmx +=1;
     for(i=1; i<=nlstate;i++)          sw += weight[i];
       for(j=1; j<=nlstate;j++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       }        } /* end of wave */
     fprintf(ficresvij,"\n");      } /* end of individual */
     free_matrix(gp,0,nhstepm,1,nlstate);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     free_matrix(gm,0,nhstepm,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (ii=1;ii<=nlstate+ndeath;ii++)
   } /* End age */            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(xp,1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_matrix(doldm,1,nlstate,1,npar);            }
   free_matrix(dnewm,1,nlstate,1,nlstate);          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
 }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 /************ Variance of prevlim ******************/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)            }
 {          
   /* Variance of prevalence limit */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double **newm;            savm=oldm;
   double **dnewm,**doldm;            oldm=newm;
   int i, j, nhstepm, hstepm;          } /* end mult */
   int k, cptcode;        
   double *xp;          s1=s[mw[mi][i]][i];
   double *gp, *gm;          s2=s[mw[mi+1][i]][i];
   double **gradg, **trgradg;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   double age,agelim;          ipmx +=1;
   int theta;          sw += weight[i];
              ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
   fprintf(ficresvpl,"# Age");        } /* end of wave */
   for(i=1; i<=nlstate;i++)      } /* end of individual */
       fprintf(ficresvpl," %1d-%1d",i,i);    } /* End of if */
   fprintf(ficresvpl,"\n");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   xp=vector(1,npar);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   dnewm=matrix(1,nlstate,1,npar);    return -l;
   doldm=matrix(1,nlstate,1,nlstate);  }
    
   hstepm=1*YEARM; /* Every year of age */  /*************** log-likelihood *************/
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  double funcone( double *x)
   agelim = AGESUP;  {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* Same as likeli but slower because of a lot of printf and if */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    int i, ii, j, k, mi, d, kk;
     if (stepm >= YEARM) hstepm=1;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double **out;
     gradg=matrix(1,npar,1,nlstate);    double lli; /* Individual log likelihood */
     gp=vector(1,nlstate);    double llt;
     gm=vector(1,nlstate);    int s1, s2;
     double bbh, survp;
     for(theta=1; theta <=npar; theta++){    /*extern weight */
       for(i=1; i<=npar; i++){ /* Computes gradient */    /* We are differentiating ll according to initial status */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       }    /*for(i=1;i<imx;i++) 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      printf(" %d\n",s[4][i]);
       for(i=1;i<=nlstate;i++)    */
         gp[i] = prlim[i][i];    cov[1]=1.;
      
       for(i=1; i<=npar; i++) /* Computes gradient */    for(k=1; k<=nlstate; k++) ll[k]=0.;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    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];
         gm[i] = prlim[i][i];      for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
       for(i=1;i<=nlstate;i++)          for (j=1;j<=nlstate+ndeath;j++){
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     } /* End theta */            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
     trgradg =matrix(1,nlstate,1,npar);        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
     for(j=1; j<=nlstate;j++)          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(theta=1; theta <=npar; theta++)          for (kk=1; kk<=cptcovage;kk++) {
         trgradg[j][theta]=gradg[theta][j];            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }
     for(i=1;i<=nlstate;i++)          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
       varpl[i][(int)age] =0.;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
     for(i=1;i<=nlstate;i++)          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          savm=oldm;
           oldm=newm;
     fprintf(ficresvpl,"%.0f ",age );        } /* end mult */
     for(i=1; i<=nlstate;i++)        
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        s1=s[mw[mi][i]][i];
     fprintf(ficresvpl,"\n");        s2=s[mw[mi+1][i]][i];
     free_vector(gp,1,nlstate);        bbh=(double)bh[mi][i]/(double)stepm; 
     free_vector(gm,1,nlstate);        /* bias is positive if real duration
     free_matrix(gradg,1,npar,1,nlstate);         * is higher than the multiple of stepm and negative otherwise.
     free_matrix(trgradg,1,nlstate,1,npar);         */
   } /* End age */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
   free_vector(xp,1,npar);        } else if  (s2==-2) {
   free_matrix(doldm,1,nlstate,1,npar);          for (j=1,survp=0. ; j<=nlstate; j++) 
   free_matrix(dnewm,1,nlstate,1,nlstate);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);
 }        }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 /************ Variance of one-step probabilities  ******************/        } else if(mle==2){
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          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 */
   int i, j, i1, k1, j1, z1;          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 */
   int k=0, cptcode;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   double **dnewm,**doldm;          lli=log(out[s1][s2]); /* Original formula */
   double *xp;        } else{  /* mle=0 back to 1 */
   double *gp, *gm;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double **gradg, **trgradg;          /*lli=log(out[s1][s2]); */ /* Original formula */
   double age,agelim, cov[NCOVMAX];        } /* End of if */
   int theta;        ipmx +=1;
   char fileresprob[FILENAMELENGTH];        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   strcpy(fileresprob,"prob");        /*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]); */
   strcat(fileresprob,fileres);        if(globpr){
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
     printf("Problem with resultfile: %s\n", fileresprob);   %11.6f %11.6f %11.6f ", \
   }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
            for(k=1,llt=0.,l=0.; k<=nlstate; k++){
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");            llt +=ll[k]*gipmx/gsw;
   fprintf(ficresprob,"# Age");            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   for(i=1; i<=nlstate;i++)          }
     for(j=1; j<=(nlstate+ndeath);j++)          fprintf(ficresilk," %10.6f\n", -llt);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);        }
       } /* end of wave */
     } /* end of individual */
   fprintf(ficresprob,"\n");    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 */
   xp=vector(1,npar);    if(globpr==0){ /* First time we count the contributions and weights */
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      gipmx=ipmx;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      gsw=sw;
      }
   cov[1]=1;    return -l;
   j=cptcoveff;  }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
   j1=0;  
   for(k1=1; k1<=1;k1++){  /*************** function likelione ***********/
     for(i1=1; i1<=ncodemax[k1];i1++){  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     j1++;  {
     /* This routine should help understanding what is done with 
     if  (cptcovn>0) {       the selection of individuals/waves and
       fprintf(ficresprob, "\n#********** Variable ");       to check the exact contribution to the likelihood.
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       Plotting could be done.
       fprintf(ficresprob, "**********\n#");     */
     }    int k;
      
       for (age=bage; age<=fage; age ++){    if(*globpri !=0){ /* Just counts and sums, no printings */
         cov[2]=age;      strcpy(fileresilk,"ilk"); 
         for (k=1; k<=cptcovn;k++) {      strcat(fileresilk,fileres);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
                  printf("Problem with resultfile: %s\n", fileresilk);
         }        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      }
         for (k=1; k<=cptcovprod;k++)      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");
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
              /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
         gradg=matrix(1,npar,1,9);      for(k=1; k<=nlstate; k++) 
         trgradg=matrix(1,9,1,npar);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    }
      
         for(theta=1; theta <=npar; theta++){    *fretone=(*funcone)(p);
           for(i=1; i<=npar; i++)    if(*globpri !=0){
             xp[i] = x[i] + (i==theta ?delti[theta]:0);      fclose(ficresilk);
                fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      fflush(fichtm); 
              } 
           k=0;    return;
           for(i=1; i<= (nlstate+ndeath); i++){  }
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;  
               gp[k]=pmmij[i][j];  /*********** Maximum Likelihood Estimation ***************/
             }  
           }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
            {
           for(i=1; i<=npar; i++)    int i,j, iter;
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    double **xi;
        double fret;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    double fretone; /* Only one call to likelihood */
           k=0;    /*  char filerespow[FILENAMELENGTH];*/
           for(i=1; i<=(nlstate+ndeath); i++){    xi=matrix(1,npar,1,npar);
             for(j=1; j<=(nlstate+ndeath);j++){    for (i=1;i<=npar;i++)
               k=k+1;      for (j=1;j<=npar;j++)
               gm[k]=pmmij[i][j];        xi[i][j]=(i==j ? 1.0 : 0.0);
             }    printf("Powell\n");  fprintf(ficlog,"Powell\n");
           }    strcpy(filerespow,"pow"); 
          strcat(filerespow,fileres);
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    if((ficrespow=fopen(filerespow,"w"))==NULL) {
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        printf("Problem with resultfile: %s\n", filerespow);
         }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    fprintf(ficrespow,"# Powell\n# iter -2*LL");
           for(theta=1; theta <=npar; theta++)    for (i=1;i<=nlstate;i++)
             trgradg[j][theta]=gradg[theta][j];      for(j=1;j<=nlstate+ndeath;j++)
                if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    fprintf(ficrespow,"\n");
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  
            powell(p,xi,npar,ftol,&iter,&fret,func);
         pmij(pmmij,cov,ncovmodel,x,nlstate);  
            free_matrix(xi,1,npar,1,npar);
         k=0;    fclose(ficrespow);
         for(i=1; i<=(nlstate+ndeath); i++){    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
           for(j=1; j<=(nlstate+ndeath);j++){    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
             k=k+1;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
             gm[k]=pmmij[i][j];  
           }  }
         }  
        /**** Computes Hessian and covariance matrix ***/
      /*printf("\n%d ",(int)age);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
      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]));    double  **a,**y,*x,pd;
      }*/    double **hess;
     int i, j,jk;
         fprintf(ficresprob,"\n%d ",(int)age);    int *indx;
   
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));    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[]) ;
       }    void ludcmp(double **a, int npar, int *indx, double *d) ;
     }    double gompertz(double p[]);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    hess=matrix(1,npar,1,npar);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    printf("\nCalculation of the hessian matrix. Wait...\n");
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   }    for (i=1;i<=npar;i++){
   free_vector(xp,1,npar);      printf("%d",i);fflush(stdout);
   fclose(ficresprob);      fprintf(ficlog,"%d",i);fflush(ficlog);
       
 }       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
 /******************* Printing html file ***********/      /*  printf(" %f ",p[i]);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
  int lastpass, int stepm, int weightopt, char model[],\    }
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\    for (i=1;i<=npar;i++) {
  char version[], int popforecast, int estepm ){      for (j=1;j<=npar;j++)  {
   int jj1, k1, i1, cpt;        if (j>i) { 
   FILE *fichtm;          printf(".%d%d",i,j);fflush(stdout);
   /*char optionfilehtm[FILENAMELENGTH];*/          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j,func,npar);
   strcpy(optionfilehtm,optionfile);          
   strcat(optionfilehtm,".htm");          hess[j][i]=hess[i][j];    
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          /*printf(" %lf ",hess[i][j]);*/
     printf("Problem with %s \n",optionfilehtm), exit(0);        }
   }      }
     }
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    printf("\n");
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    fprintf(ficlog,"\n");
 \n  
 Total number of observations=%d <br>\n    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 <hr  size=\"2\" color=\"#EC5E5E\">    
  <ul><li>Outputs files<br>\n    a=matrix(1,npar,1,npar);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    y=matrix(1,npar,1,npar);
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n    x=vector(1,npar);
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    indx=ivector(1,npar);
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    for (i=1;i<=npar;i++)
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    ludcmp(a,npar,indx,&pd);
   
  fprintf(fichtm,"\n    for (j=1;j<=npar;j++) {
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n      for (i=1;i<=npar;i++) x[i]=0;
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      x[j]=1;
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      lubksb(a,npar,indx,x);
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n      for (i=1;i<=npar;i++){ 
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);        matcov[i][j]=x[i];
       }
  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    printf("\n#Hessian matrix#\n");
         <br>",fileres,fileres,fileres,fileres);    fprintf(ficlog,"\n#Hessian matrix#\n");
  else    for (i=1;i<=npar;i++) { 
    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);      for (j=1;j<=npar;j++) { 
 fprintf(fichtm," <li>Graphs</li><p>");        printf("%.3e ",hess[i][j]);
         fprintf(ficlog,"%.3e ",hess[i][j]);
  m=cptcoveff;      }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      printf("\n");
       fprintf(ficlog,"\n");
  jj1=0;    }
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){    /* Recompute Inverse */
        jj1++;    for (i=1;i<=npar;i++)
        if (cptcovn > 0) {      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    ludcmp(a,npar,indx,&pd);
          for (cpt=1; cpt<=cptcoveff;cpt++)  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    /*  printf("\n#Hessian matrix recomputed#\n");
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
        }    for (j=1;j<=npar;j++) {
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      for (i=1;i<=npar;i++) x[i]=0;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          x[j]=1;
        for(cpt=1; cpt<nlstate;cpt++){      lubksb(a,npar,indx,x);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      for (i=1;i<=npar;i++){ 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        y[i][j]=x[i];
        }        printf("%.3e ",y[i][j]);
     for(cpt=1; cpt<=nlstate;cpt++) {        fprintf(ficlog,"%.3e ",y[i][j]);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      }
 interval) in state (%d): v%s%d%d.gif <br>      printf("\n");
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        fprintf(ficlog,"\n");
      }    }
      for(cpt=1; cpt<=nlstate;cpt++) {    */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    free_matrix(a,1,npar,1,npar);
      }    free_matrix(y,1,npar,1,npar);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    free_vector(x,1,npar);
 health expectancies in states (1) and (2): e%s%d.gif<br>    free_ivector(indx,1,npar);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    free_matrix(hess,1,npar,1,npar);
 fprintf(fichtm,"\n</body>");  
    }  
    }  }
 fclose(fichtm);  
 }  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 /******************* Gnuplot file **************/  {
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    int i;
     int l=1, lmax=20;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    double k1,k2;
     double p2[MAXPARM+1]; /* identical to x */
   strcpy(optionfilegnuplot,optionfilefiname);    double res;
   strcat(optionfilegnuplot,".gp.txt");    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    double fx;
     printf("Problem with file %s",optionfilegnuplot);    int k=0,kmax=10;
   }    double l1;
   
 #ifdef windows    fx=func(x);
     fprintf(ficgp,"cd \"%s\" \n",pathc);    for (i=1;i<=npar;i++) p2[i]=x[i];
 #endif    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
 m=pow(2,cptcoveff);      l1=pow(10,l);
        delts=delt;
  /* 1eme*/      for(k=1 ; k <kmax; k=k+1){
   for (cpt=1; cpt<= nlstate ; cpt ++) {        delt = delta*(l1*k);
    for (k1=1; k1<= m ; k1 ++) {        p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
 #ifdef windows        p2[theta]=x[theta]-delt;
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);        k2=func(p2)-fx;
 #endif        /*res= (k1-2.0*fx+k2)/delt/delt; */
 #ifdef unix        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        
 #endif  #ifdef DEBUGHESS
         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);
 for (i=1; i<= nlstate ; i ++) {        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);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  #endif
   else fprintf(ficgp," \%%*lf (\%%*lf)");        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          k=kmax;
     for (i=1; i<= nlstate ; i ++) {        }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   else fprintf(ficgp," \%%*lf (\%%*lf)");          k=kmax; l=lmax*10.;
 }        }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
      for (i=1; i<= nlstate ; i ++) {          delts=delt;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");      }
 }      }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    delti[theta]=delts;
 #ifdef unix    return res; 
 fprintf(ficgp,"\nset ter gif small size 400,300");    
 #endif  }
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
    }  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   }  {
   /*2 eme*/    int i;
     int l=1, l1, lmax=20;
   for (k1=1; k1<= m ; k1 ++) {    double k1,k2,k3,k4,res,fx;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    double p2[MAXPARM+1];
        int k;
     for (i=1; i<= nlstate+1 ; i ++) {  
       k=2*i;    fx=func(x);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    for (k=1; k<=2; k++) {
       for (j=1; j<= nlstate+1 ; j ++) {      for (i=1;i<=npar;i++) p2[i]=x[i];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      p2[thetai]=x[thetai]+delti[thetai]/k;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 }        k1=func(p2)-fx;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      p2[thetai]=x[thetai]+delti[thetai]/k;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for (j=1; j<= nlstate+1 ; j ++) {      k2=func(p2)-fx;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    
         else fprintf(ficgp," \%%*lf (\%%*lf)");      p2[thetai]=x[thetai]-delti[thetai]/k;
 }        p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       fprintf(ficgp,"\" t\"\" w l 0,");      k3=func(p2)-fx;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    
       for (j=1; j<= nlstate+1 ; j ++) {      p2[thetai]=x[thetai]-delti[thetai]/k;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      k4=func(p2)-fx;
 }        res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  #ifdef DEBUG
       else fprintf(ficgp,"\" t\"\" w l 0,");      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);
     }      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);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  #endif
   }    }
      return res;
   /*3eme*/  }
   
   for (k1=1; k1<= m ; k1 ++) {  /************** Inverse of matrix **************/
     for (cpt=1; cpt<= nlstate ; cpt ++) {  void ludcmp(double **a, int n, int *indx, double *d) 
       k=2+nlstate*(2*cpt-2);  { 
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    int i,imax,j,k; 
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    double big,dum,sum,temp; 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    double *vv; 
 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);    vv=vector(1,n); 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    *d=1.0; 
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    for (i=1;i<=n;i++) { 
       big=0.0; 
 */      for (j=1;j<=n;j++) 
       for (i=1; i< nlstate ; i ++) {        if ((temp=fabs(a[i][j])) > big) big=temp; 
         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);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
       }    } 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    for (j=1;j<=n;j++) { 
     }      for (i=1;i<j;i++) { 
     }        sum=a[i][j]; 
          for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   /* CV preval stat */        a[i][j]=sum; 
     for (k1=1; k1<= m ; k1 ++) {      } 
     for (cpt=1; cpt<nlstate ; cpt ++) {      big=0.0; 
       k=3;      for (i=j;i<=n;i++) { 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        sum=a[i][j]; 
         for (k=1;k<j;k++) 
       for (i=1; i< nlstate ; i ++)          sum -= a[i][k]*a[k][j]; 
         fprintf(ficgp,"+$%d",k+i+1);        a[i][j]=sum; 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
                big=dum; 
       l=3+(nlstate+ndeath)*cpt;          imax=i; 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        } 
       for (i=1; i< nlstate ; i ++) {      } 
         l=3+(nlstate+ndeath)*cpt;      if (j != imax) { 
         fprintf(ficgp,"+$%d",l+i+1);        for (k=1;k<=n;k++) { 
       }          dum=a[imax][k]; 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            a[imax][k]=a[j][k]; 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          a[j][k]=dum; 
     }        } 
   }          *d = -(*d); 
          vv[imax]=vv[j]; 
   /* proba elementaires */      } 
    for(i=1,jk=1; i <=nlstate; i++){      indx[j]=imax; 
     for(k=1; k <=(nlstate+ndeath); k++){      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (k != i) {      if (j != n) { 
         for(j=1; j <=ncovmodel; j++){        dum=1.0/(a[j][j]); 
                for (i=j+1;i<=n;i++) a[i][j] *= dum; 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      } 
           jk++;    } 
           fprintf(ficgp,"\n");    free_vector(vv,1,n);  /* Doesn't work */
         }  ;
       }  } 
     }  
     }  void lubksb(double **a, int n, int *indx, double b[]) 
   { 
     for(jk=1; jk <=m; jk++) {    int i,ii=0,ip,j; 
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    double sum; 
    i=1;   
    for(k2=1; k2<=nlstate; k2++) {    for (i=1;i<=n;i++) { 
      k3=i;      ip=indx[i]; 
      for(k=1; k<=(nlstate+ndeath); k++) {      sum=b[ip]; 
        if (k != k2){      b[ip]=b[i]; 
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      if (ii) 
 ij=1;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         for(j=3; j <=ncovmodel; j++) {      else if (sum) ii=i; 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      b[i]=sum; 
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    } 
             ij++;    for (i=n;i>=1;i--) { 
           }      sum=b[i]; 
           else      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      b[i]=sum/a[i][i]; 
         }    } 
           fprintf(ficgp,")/(1");  } 
          
         for(k1=1; k1 <=nlstate; k1++){    void pstamp(FILE *fichier)
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  {
 ij=1;    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
           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]]]);  /************ Frequencies ********************/
             ij++;  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
           }  {  /* Some frequencies */
           else    
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    int i, m, jk, k1,i1, j1, bool, z1,j;
           }    int first;
           fprintf(ficgp,")");    double ***freq; /* Frequencies */
         }    double *pp, **prop;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    char fileresp[FILENAMELENGTH];
         i=i+ncovmodel;    
        }    pp=vector(1,nlstate);
      }    prop=matrix(1,nlstate,iagemin,iagemax+3);
    }    strcpy(fileresp,"p");
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    strcat(fileresp,fileres);
    }    if((ficresp=fopen(fileresp,"w"))==NULL) {
          printf("Problem with prevalence resultfile: %s\n", fileresp);
   fclose(ficgp);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 }  /* end gnuplot */      exit(0);
     }
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
 /*************** Moving average **************/    j1=0;
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    
     j=cptcoveff;
   int i, cpt, cptcod;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)  
       for (i=1; i<=nlstate;i++)    first=1;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  
           mobaverage[(int)agedeb][i][cptcod]=0.;    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
        /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    /*    j1++;
       for (i=1; i<=nlstate;i++){  */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
           for (cpt=0;cpt<=4;cpt++){        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          scanf("%d", i);*/
           }        for (i=-5; i<=nlstate+ndeath; i++)  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
         }            for(m=iagemin; m <= iagemax+3; m++)
       }              freq[i][jk][m]=0;
     }        
            for (i=1; i<=nlstate; i++)  
 }          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0;
         
 /************** Forecasting ******************/        dateintsum=0;
 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){        k2cpt=0;
          for (i=1; i<=imx; i++) {
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          bool=1;
   int *popage;          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            for (z1=1; z1<=cptcoveff; z1++)       
   double *popeffectif,*popcount;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
   double ***p3mat;                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
   char fileresf[FILENAMELENGTH];                bool=0;
                 /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
  agelim=AGESUP;                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;                  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*/
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              } 
            }
     
   strcpy(fileresf,"f");          if (bool==1){
   strcat(fileresf,fileres);            for(m=firstpass; m<=lastpass; m++){
   if((ficresf=fopen(fileresf,"w"))==NULL) {              k2=anint[m][i]+(mint[m][i]/12.);
     printf("Problem with forecast resultfile: %s\n", fileresf);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   printf("Computing forecasting: result on file '%s' \n", fileresf);                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];
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   if (mobilav==1) {                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                }
     movingaverage(agedeb, fage, ageminpar, mobaverage);                
   }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
   stepsize=(int) (stepm+YEARM-1)/YEARM;                  k2cpt++;
   if (stepm<=12) stepsize=1;                }
                  /*}*/
   agelim=AGESUP;            }
            }
   hstepm=1;        } /* end i */
   hstepm=hstepm/stepm;         
   yp1=modf(dateintmean,&yp);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   anprojmean=yp;        pstamp(ficresp);
   yp2=modf((yp1*12),&yp);        if  (cptcovn>0) {
   mprojmean=yp;          fprintf(ficresp, "\n#********** Variable "); 
   yp1=modf((yp2*30.5),&yp);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   jprojmean=yp;          fprintf(ficresp, "**********\n#");
   if(jprojmean==0) jprojmean=1;          fprintf(ficlog, "\n#********** Variable "); 
   if(mprojmean==0) jprojmean=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficlog, "**********\n#");
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        }
          for(i=1; i<=nlstate;i++) 
   for(cptcov=1;cptcov<=i2;cptcov++){          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        fprintf(ficresp, "\n");
       k=k+1;        
       fprintf(ficresf,"\n#******");        for(i=iagemin; i <= iagemax+3; i++){
       for(j=1;j<=cptcoveff;j++) {          if(i==iagemax+3){
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficlog,"Total");
       }          }else{
       fprintf(ficresf,"******\n");            if(first==1){
       fprintf(ficresf,"# StartingAge FinalAge");              first=0;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);              printf("See log file for details...\n");
                  }
                  fprintf(ficlog,"Age %d", i);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {          }
         fprintf(ficresf,"\n");          for(jk=1; jk <=nlstate ; jk++){
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          for(jk=1; jk <=nlstate ; jk++){
           nhstepm = nhstepm/hstepm;            for(m=-1, pos=0; m <=0 ; m++)
                        pos += freq[jk][m][i];
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if(pp[jk]>=1.e-10){
           oldm=oldms;savm=savms;              if(first==1){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                      }
           for (h=0; h<=nhstepm; h++){              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             if (h==(int) (calagedate+YEARM*cpt)) {            }else{
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);              if(first==1)
             }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             for(j=1; j<=nlstate+ndeath;j++) {              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               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];          for(jk=1; jk <=nlstate ; jk++){
                 else {            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              pp[jk] += freq[jk][m][i];
                 }          }       
                          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
               }            pos += pp[jk];
               if (h==(int)(calagedate+12*cpt)){            posprop += prop[jk][i];
                 fprintf(ficresf," %.3f", kk1);          }
                                  for(jk=1; jk <=nlstate ; jk++){
               }            if(pos>=1.e-5){
             }              if(first==1)
           }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         }            }else{
       }              if(first==1)
     }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                    }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            if( i <= iagemax){
               if(pos>=1.e-5){
   fclose(ficresf);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
 }                /*probs[i][jk][j1]= pp[jk]/pos;*/
 /************** Forecasting ******************/                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 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){              }
                else
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   int *popage;            }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          }
   double *popeffectif,*popcount;          
   double ***p3mat,***tabpop,***tabpopprev;          for(jk=-1; jk <=nlstate+ndeath; jk++)
   char filerespop[FILENAMELENGTH];            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              if(first==1)
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   agelim=AGESUP;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;              }
            if(i <= iagemax)
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            fprintf(ficresp,"\n");
            if(first==1)
              printf("Others in log...\n");
   strcpy(filerespop,"pop");          fprintf(ficlog,"\n");
   strcat(filerespop,fileres);        }
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        /*}*/
     printf("Problem with forecast resultfile: %s\n", filerespop);    }
   }    dateintmean=dateintsum/k2cpt; 
   printf("Computing forecasting: result on file '%s' \n", filerespop);   
     fclose(ficresp);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
   if (mobilav==1) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* End of Freq */
     movingaverage(agedeb, fage, ageminpar, mobaverage);  }
   }  
   /************ Prevalence ********************/
   stepsize=(int) (stepm+YEARM-1)/YEARM;  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)
   if (stepm<=12) stepsize=1;  {  
      /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   agelim=AGESUP;       in each health status at the date of interview (if between dateprev1 and dateprev2).
         We still use firstpass and lastpass as another selection.
   hstepm=1;    */
   hstepm=hstepm/stepm;   
      int i, m, jk, k1, i1, j1, bool, z1,j;
   if (popforecast==1) {    double ***freq; /* Frequencies */
     if((ficpop=fopen(popfile,"r"))==NULL) {    double *pp, **prop;
       printf("Problem with population file : %s\n",popfile);exit(0);    double pos,posprop; 
     }    double  y2; /* in fractional years */
     popage=ivector(0,AGESUP);    int iagemin, iagemax;
     popeffectif=vector(0,AGESUP);    int first; /** to stop verbosity which is redirected to log file */
     popcount=vector(0,AGESUP);  
        iagemin= (int) agemin;
     i=1;      iagemax= (int) agemax;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    /*pp=vector(1,nlstate);*/
        prop=matrix(1,nlstate,iagemin,iagemax+3); 
     imx=i;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    j1=0;
   }    
     /*j=cptcoveff;*/
   for(cptcov=1;cptcov<=i2;cptcov++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    
       k=k+1;    first=1;
       fprintf(ficrespop,"\n#******");    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
       for(j=1;j<=cptcoveff;j++) {      /*for(i1=1; i1<=ncodemax[k1];i1++){
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        j1++;*/
       }        
       fprintf(ficrespop,"******\n");        for (i=1; i<=nlstate; i++)  
       fprintf(ficrespop,"# Age");          for(m=iagemin; m <= iagemax+3; m++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);            prop[i][m]=0.0;
       if (popforecast==1)  fprintf(ficrespop," [Population]");       
              for (i=1; i<=imx; i++) { /* Each individual */
       for (cpt=0; cpt<=0;cpt++) {          bool=1;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            if  (cptcovn>0) {
                    for (z1=1; z1<=cptcoveff; z1++) 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                bool=0;
           nhstepm = nhstepm/hstepm;          } 
                    if (bool==1) { 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           oldm=oldms;savm=savms;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                        if(agev[m][i]==0) agev[m][i]=iagemax+1;
           for (h=0; h<=nhstepm; h++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             if (h==(int) (calagedate+YEARM*cpt)) {                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); 
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
             }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
             for(j=1; j<=nlstate+ndeath;j++) {                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
               kk1=0.;kk2=0;                  prop[s[m][i]][iagemax+3] += weight[i]; 
               for(i=1; i<=nlstate;i++) {                              } 
                 if (mobilav==1)              }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            } /* end selection of waves */
                 else {          }
                   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]; 
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          } 
                   /*fprintf(ficrespop," %.3f", kk1);          
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          for(jk=1; jk <=nlstate ; jk++){     
               }            if( i <=  iagemax){ 
             }              if(posprop>=1.e-5){ 
             for(i=1; i<=nlstate;i++){                probs[i][jk][j1]= prop[jk][i]/posprop;
               kk1=0.;              } else{
                 for(j=1; j<=nlstate;j++){                if(first==1){
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];                  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]);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];                }
             }              }
             } 
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          }/* end jk */ 
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        }/* end i */ 
           }      /*} *//* end i1 */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    } /* end j1 */
         }    
       }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
      /*free_vector(pp,1,nlstate);*/
   /******/    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    /************* Waves Concatenation ***************/
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  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)
           nhstepm = nhstepm/hstepm;  {
              /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       Death is a valid wave (if date is known).
           oldm=oldms;savm=savms;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
           for (h=0; h<=nhstepm; h++){       and mw[mi+1][i]. dh depends on stepm.
             if (h==(int) (calagedate+YEARM*cpt)) {       */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }    int i, mi, m;
             for(j=1; j<=nlstate+ndeath;j++) {    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
               kk1=0.;kk2=0;       double sum=0., jmean=0.;*/
               for(i=1; i<=nlstate;i++) {                  int first;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        int j, k=0,jk, ju, jl;
               }    double sum=0.;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    first=0;
             }    jmin=1e+5;
           }    jmax=-1;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    jmean=0.;
         }    for(i=1; i<=imx; i++){
       }      mi=0;
    }      m=firstpass;
   }      while(s[m][i] <= nlstate){
          if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          mw[++mi][i]=m;
         if(m >=lastpass)
   if (popforecast==1) {          break;
     free_ivector(popage,0,AGESUP);        else
     free_vector(popeffectif,0,AGESUP);          m++;
     free_vector(popcount,0,AGESUP);      }/* end while */
   }      if (s[m][i] > nlstate){
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        mi++;     /* Death is another wave */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        /* if(mi==0)  never been interviewed correctly before death */
   fclose(ficrespop);           /* Only death is a correct wave */
 }        mw[mi][i]=m;
       }
 /***********************************************/  
 /**************** Main Program *****************/      wav[i]=mi;
 /***********************************************/      if(mi==0){
         nbwarn++;
 int main(int argc, char *argv[])        if(first==0){
 {          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           first=1;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        }
   double agedeb, agefin,hf;        if(first==1){
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         }
   double fret;      } /* end mi==0 */
   double **xi,tmp,delta;    } /* End individuals */
   
   double dum; /* Dummy variable */    for(i=1; i<=imx; i++){
   double ***p3mat;      for(mi=1; mi<wav[i];mi++){
   int *indx;        if (stepm <=0)
   char line[MAXLINE], linepar[MAXLINE];          dh[mi][i]=1;
   char title[MAXLINE];        else{
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];            if (agedc[i] < 2*AGESUP) {
                j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];              if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
   char filerest[FILENAMELENGTH];                nberr++;
   char fileregp[FILENAMELENGTH];                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]);
   char popfile[FILENAMELENGTH];                j=1; /* Temporary Dangerous patch */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                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);
   int firstobs=1, lastobs=10;                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]);
   int sdeb, sfin; /* Status at beginning and end */                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);
   int c,  h , cpt,l;              }
   int ju,jl, mi;              k=k+1;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;              if (j >= jmax){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                jmax=j;
   int mobilav=0,popforecast=0;                ijmax=i;
   int hstepm, nhstepm;              }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;              if (j <= jmin){
                 jmin=j;
   double bage, fage, age, agelim, agebase;                ijmin=i;
   double ftolpl=FTOL;              }
   double **prlim;              sum=sum+j;
   double *severity;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   double ***param; /* Matrix of parameters */              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   double  *p;            }
   double **matcov; /* Matrix of covariance */          }
   double ***delti3; /* Scale */          else{
   double *delti; /* Scale */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   double ***eij, ***vareij;  /*        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]); */
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;            k=k+1;
   double kk1, kk2;            if (j >= jmax) {
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;              jmax=j;
                ijmax=i;
             }
   char version[80]="Imach version 0.8a, May 2002, INED-EUROREVES ";            else if (j <= jmin){
   char *alph[]={"a","a","b","c","d","e"}, str[4];              jmin=j;
               ijmin=i;
             }
   char z[1]="c", occ;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 #include <sys/time.h>            /*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]);*/
 #include <time.h>            if(j<0){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];              nberr++;
                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]);
   /* long total_usecs;              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]);
   struct timeval start_time, end_time;            }
              sum=sum+j;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          }
   getcwd(pathcd, size);          jk= j/stepm;
           jl= j -jk*stepm;
   printf("\n%s",version);          ju= j -(jk+1)*stepm;
   if(argc <=1){          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     printf("\nEnter the parameter file name: ");            if(jl==0){
     scanf("%s",pathtot);              dh[mi][i]=jk;
   }              bh[mi][i]=0;
   else{            }else{ /* We want a negative bias in order to only have interpolation ie
     strcpy(pathtot,argv[1]);                    * to avoid the price of an extra matrix product in likelihood */
   }              dh[mi][i]=jk+1;
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/              bh[mi][i]=ju;
   /*cygwin_split_path(pathtot,path,optionfile);            }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          }else{
   /* cutv(path,optionfile,pathtot,'\\');*/            if(jl <= -ju){
               dh[mi][i]=jk;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);              bh[mi][i]=jl;       /* bias is positive if real duration
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                                   * is higher than the multiple of stepm and negative otherwise.
   chdir(path);                                   */
   replace(pathc,path);            }
             else{
 /*-------- arguments in the command line --------*/              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
   strcpy(fileres,"r");            }
   strcat(fileres, optionfilefiname);            if(dh[mi][i]==0){
   strcat(fileres,".txt");    /* Other files have txt extension */              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
   /*---------arguments file --------*/              /*  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((ficpar=fopen(optionfile,"r"))==NULL)    {          } /* end if mle */
     printf("Problem with optionfile %s\n",optionfile);        }
     goto end;      } /* end wave */
   }    }
     jmean=sum/k;
   strcpy(filereso,"o");    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);
   strcat(filereso,fileres);    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);
   if((ficparo=fopen(filereso,"w"))==NULL) {   }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }  /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   /* Reads comments: lines beginning with '#' */  {
   while((c=getc(ficpar))=='#' && c!= EOF){    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
     ungetc(c,ficpar);    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
     fgets(line, MAXLINE, ficpar);    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
     puts(line);     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
     fputs(line,ficparo);    /* nbcode[Tvar[j]][1]= 
   }    */
   ungetc(c,ficpar);  
     int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   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);    int modmaxcovj=0; /* Modality max of covariates j */
   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);    int cptcode=0; /* Modality max of covariates j */
   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);    int modmincovj=0; /* Modality min of covariates j */
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    cptcoveff=0; 
     puts(line);   
     fputs(line,ficparo);    for (k=-1; k < maxncov; k++) Ndum[k]=0;
   }    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   ungetc(c,ficpar);  
      /* Loop on covariates without age and products */
        for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
   covar=matrix(0,NCOVMAX,1,n);      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
   cptcovn=0;                                 modality of this covariate Vj*/ 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        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 *:
   ncovmodel=2+cptcovn;                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
          /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
   /* Read guess parameters */                                        modality of the nth covariate of individual i. */
   /* Reads comments: lines beginning with '#' */        if (ij > modmaxcovj)
   while((c=getc(ficpar))=='#' && c!= EOF){          modmaxcovj=ij; 
     ungetc(c,ficpar);        else if (ij < modmincovj) 
     fgets(line, MAXLINE, ficpar);          modmincovj=ij; 
     puts(line);        if ((ij < -1) && (ij > NCOVMAX)){
     fputs(line,ficparo);          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   }          exit(1);
   ungetc(c,ficpar);        }else
          Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
     for(i=1; i <=nlstate; i++)        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     for(j=1; j <=nlstate+ndeath-1; j++){        /* getting the maximum value of the modality of the covariate
       fscanf(ficpar,"%1d%1d",&i1,&j1);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
       fprintf(ficparo,"%1d%1d",i1,j1);           female is 1, then modmaxcovj=1.*/
       printf("%1d%1d",i,j);      }
       for(k=1; k<=ncovmodel;k++){      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
         fscanf(ficpar," %lf",&param[i][j][k]);      cptcode=modmaxcovj;
         printf(" %lf",param[i][j][k]);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
         fprintf(ficparo," %lf",param[i][j][k]);     /*for (i=0; i<=cptcode; i++) {*/
       }      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
       fscanf(ficpar,"\n");        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
       printf("\n");        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
       fprintf(ficparo,"\n");          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
     }        }
          /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
       } /* Ndum[-1] number of undefined modalities */
   p=param[1][1];  
        /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
   /* Reads comments: lines beginning with '#' */      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
   while((c=getc(ficpar))=='#' && c!= EOF){      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
     ungetc(c,ficpar);         modmincovj=3; modmaxcovj = 7;
     fgets(line, MAXLINE, ficpar);         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
     puts(line);         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
     fputs(line,ficparo);         variables V1_1 and V1_2.
   }         nbcode[Tvar[j]][ij]=k;
   ungetc(c,ficpar);         nbcode[Tvar[j]][1]=0;
          nbcode[Tvar[j]][2]=1;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);         nbcode[Tvar[j]][3]=2;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      */
   for(i=1; i <=nlstate; i++){      ij=1; /* ij is similar to i but can jumps over null modalities */
     for(j=1; j <=nlstate+ndeath-1; j++){      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
       fscanf(ficpar,"%1d%1d",&i1,&j1);        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
       printf("%1d%1d",i,j);          /*recode from 0 */
       fprintf(ficparo,"%1d%1d",i1,j1);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
       for(k=1; k<=ncovmodel;k++){            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
         fscanf(ficpar,"%le",&delti3[i][j][k]);                                       k is a modality. If we have model=V1+V1*sex 
         printf(" %le",delti3[i][j][k]);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
         fprintf(ficparo," %le",delti3[i][j][k]);            ij++;
       }          }
       fscanf(ficpar,"\n");          if (ij > ncodemax[j]) break; 
       printf("\n");        }  /* end of loop on */
       fprintf(ficparo,"\n");      } /* 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*/  
   }    
   delti=delti3[1][1];   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
      
   /* Reads comments: lines beginning with '#' */    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
   while((c=getc(ficpar))=='#' && c!= EOF){     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
     ungetc(c,ficpar);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
     fgets(line, MAXLINE, ficpar);     Ndum[ij]++; 
     puts(line);   } 
     fputs(line,ficparo);  
   }   ij=1;
   ungetc(c,ficpar);   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
       /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   matcov=matrix(1,npar,1,npar);     if((Ndum[i]!=0) && (i<=ncovcol)){
   for(i=1; i <=npar; i++){       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
     fscanf(ficpar,"%s",&str);       Tvaraff[ij]=i; /*For printing (unclear) */
     printf("%s",str);       ij++;
     fprintf(ficparo,"%s",str);     }else
     for(j=1; j <=i; j++){         Tvaraff[ij]=0;
       fscanf(ficpar," %le",&matcov[i][j]);   }
       printf(" %.5le",matcov[i][j]);   ij--;
       fprintf(ficparo," %.5le",matcov[i][j]);   cptcoveff=ij; /*Number of total covariates*/
     }  
     fscanf(ficpar,"\n");  }
     printf("\n");  
     fprintf(ficparo,"\n");  
   }  /*********** Health Expectancies ****************/
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
       matcov[i][j]=matcov[j][i];  
      {
   printf("\n");    /* Health expectancies, no variances */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     int nhstepma, nstepma; /* Decreasing with age */
     /*-------- Rewriting paramater file ----------*/    double age, agelim, hf;
      strcpy(rfileres,"r");    /* "Rparameterfile */    double ***p3mat;
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    double eip;
      strcat(rfileres,".");    /* */  
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    pstamp(ficreseij);
     if((ficres =fopen(rfileres,"w"))==NULL) {    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    fprintf(ficreseij,"# Age");
     }    for(i=1; i<=nlstate;i++){
     fprintf(ficres,"#%s\n",version);      for(j=1; j<=nlstate;j++){
            fprintf(ficreseij," e%1d%1d ",i,j);
     /*-------- data file ----------*/      }
     if((fic=fopen(datafile,"r"))==NULL)    {      fprintf(ficreseij," e%1d. ",i);
       printf("Problem with datafile: %s\n", datafile);goto end;    }
     }    fprintf(ficreseij,"\n");
   
     n= lastobs;    
     severity = vector(1,maxwav);    if(estepm < stepm){
     outcome=imatrix(1,maxwav+1,1,n);      printf ("Problem %d lower than %d\n",estepm, stepm);
     num=ivector(1,n);    }
     moisnais=vector(1,n);    else  hstepm=estepm;   
     annais=vector(1,n);    /* We compute the life expectancy from trapezoids spaced every estepm months
     moisdc=vector(1,n);     * This is mainly to measure the difference between two models: for example
     andc=vector(1,n);     * if stepm=24 months pijx are given only every 2 years and by summing them
     agedc=vector(1,n);     * we are calculating an estimate of the Life Expectancy assuming a linear 
     cod=ivector(1,n);     * progression in between and thus overestimating or underestimating according
     weight=vector(1,n);     * to the curvature of the survival function. If, for the same date, we 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     mint=matrix(1,maxwav,1,n);     * to compare the new estimate of Life expectancy with the same linear 
     anint=matrix(1,maxwav,1,n);     * hypothesis. A more precise result, taking into account a more precise
     s=imatrix(1,maxwav+1,1,n);     * curvature will be obtained if estepm is as small as stepm. */
     adl=imatrix(1,maxwav+1,1,n);      
     tab=ivector(1,NCOVMAX);    /* For example we decided to compute the life expectancy with the smallest unit */
     ncodemax=ivector(1,8);    /* 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 
     i=1;       nstepm is the number of stepm from age to agelin. 
     while (fgets(line, MAXLINE, fic) != NULL)    {       Look at hpijx to understand the reason of that which relies in memory size
       if ((i >= firstobs) && (i <=lastobs)) {       and note for a fixed period like estepm months */
            /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         for (j=maxwav;j>=1;j--){       survival function given by stepm (the optimization length). Unfortunately it
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);       means that if the survival funtion is printed only each two years of age and if
           strcpy(line,stra);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);       results. So we changed our mind and took the option of the best precision.
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    */
         }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    agelim=AGESUP;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      
   /* nhstepm age range expressed in number of stepm */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         for (j=ncovcol;j>=1;j--){    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    /* if (stepm >= YEARM) hstepm=1;*/
         }    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         num[i]=atol(stra);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    for (age=bage; age<=fage; age ++){ 
           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;}*/      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         i=i+1;      /* if (stepm >= YEARM) hstepm=1;*/
       }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     }  
     /* printf("ii=%d", ij);      /* If stepm=6 months */
        scanf("%d",i);*/      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   imx=i-1; /* Number of individuals */         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
   /* for (i=1; i<=imx; i++){      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      
     }*/      printf("%d|",(int)age);fflush(stdout);
    /*  for (i=1; i<=imx; i++){      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
      if (s[4][i]==9)  s[4][i]=-1;      
      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]));}*/      /* Computing expectancies */
        for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
   /* Calculation of the number of parameter from char model*/          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   Tvar=ivector(1,15);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   Tprod=ivector(1,15);            
   Tvaraff=ivector(1,15);            /* 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]);*/
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);                }
      
   if (strlen(model) >1){      fprintf(ficreseij,"%3.0f",age );
     j=0, j1=0, k1=1, k2=1;      for(i=1; i<=nlstate;i++){
     j=nbocc(model,'+');        eip=0;
     j1=nbocc(model,'*');        for(j=1; j<=nlstate;j++){
     cptcovn=j+1;          eip +=eij[i][j][(int)age];
     cptcovprod=j1;          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
            }
     strcpy(modelsav,model);        fprintf(ficreseij,"%9.4f", eip );
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      }
       printf("Error. Non available option model=%s ",model);      fprintf(ficreseij,"\n");
       goto end;      
     }    }
        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for(i=(j+1); i>=1;i--){    printf("\n");
       cutv(stra,strb,modelsav,'+');    fprintf(ficlog,"\n");
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  }
       /*scanf("%d",i);*/  
       if (strchr(strb,'*')) {  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[] )
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {  {
           cptcovprod--;    /* Covariances of health expectancies eij and of total life expectancies according
           cutv(strb,stre,strd,'V');     to initial status i, ei. .
           Tvar[i]=atoi(stre);    */
           cptcovage++;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
             Tage[cptcovage]=i;    int nhstepma, nstepma; /* Decreasing with age */
             /*printf("stre=%s ", stre);*/    double age, agelim, hf;
         }    double ***p3matp, ***p3matm, ***varhe;
         else if (strcmp(strd,"age")==0) {    double **dnewm,**doldm;
           cptcovprod--;    double *xp, *xm;
           cutv(strb,stre,strc,'V');    double **gp, **gm;
           Tvar[i]=atoi(stre);    double ***gradg, ***trgradg;
           cptcovage++;    int theta;
           Tage[cptcovage]=i;  
         }    double eip, vip;
         else {  
           cutv(strb,stre,strc,'V');    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
           Tvar[i]=ncovcol+k1;    xp=vector(1,npar);
           cutv(strb,strc,strd,'V');    xm=vector(1,npar);
           Tprod[k1]=i;    dnewm=matrix(1,nlstate*nlstate,1,npar);
           Tvard[k1][1]=atoi(strc);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
           Tvard[k1][2]=atoi(stre);    
           Tvar[cptcovn+k2]=Tvard[k1][1];    pstamp(ficresstdeij);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
           for (k=1; k<=lastobs;k++)    fprintf(ficresstdeij,"# Age");
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    for(i=1; i<=nlstate;i++){
           k1++;      for(j=1; j<=nlstate;j++)
           k2=k2+2;        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
         }      fprintf(ficresstdeij," e%1d. ",i);
       }    }
       else {    fprintf(ficresstdeij,"\n");
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  
        /*  scanf("%d",i);*/    pstamp(ficrescveij);
       cutv(strd,strc,strb,'V');    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
       Tvar[i]=atoi(strc);    fprintf(ficrescveij,"# Age");
       }    for(i=1; i<=nlstate;i++)
       strcpy(modelsav,stra);        for(j=1; j<=nlstate;j++){
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        cptj= (j-1)*nlstate+i;
         scanf("%d",i);*/        for(i2=1; i2<=nlstate;i2++)
     }          for(j2=1; j2<=nlstate;j2++){
 }            cptj2= (j2-1)*nlstate+i2;
              if(cptj2 <= cptj)
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
   printf("cptcovprod=%d ", cptcovprod);          }
   scanf("%d ",i);*/      }
     fclose(fic);    fprintf(ficrescveij,"\n");
     
     /*  if(mle==1){*/    if(estepm < stepm){
     if (weightopt != 1) { /* Maximisation without weights*/      printf ("Problem %d lower than %d\n",estepm, stepm);
       for(i=1;i<=n;i++) weight[i]=1.0;    }
     }    else  hstepm=estepm;   
     /*-calculation of age at interview from date of interview and age at death -*/    /* We compute the life expectancy from trapezoids spaced every estepm months
     agev=matrix(1,maxwav,1,imx);     * 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
     for (i=1; i<=imx; i++) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
       for(m=2; (m<= maxwav); m++) {     * progression in between and thus overestimating or underestimating according
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){     * to the curvature of the survival function. If, for the same date, we 
          anint[m][i]=9999;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
          s[m][i]=-1;     * to compare the new estimate of Life expectancy with the same linear 
        }     * hypothesis. A more precise result, taking into account a more precise
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;     * curvature will be obtained if estepm is as small as stepm. */
       }  
     }    /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     for (i=1; i<=imx; i++)  {       nhstepm is the number of hstepm from age to agelim 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);       nstepm is the number of stepm from age to agelin. 
       for(m=1; (m<= maxwav); m++){       Look at hpijx to understand the reason of that which relies in memory size
         if(s[m][i] >0){       and note for a fixed period like estepm months */
           if (s[m][i] >= nlstate+1) {    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
             if(agedc[i]>0)       survival function given by stepm (the optimization length). Unfortunately it
               if(moisdc[i]!=99 && andc[i]!=9999)       means that if the survival funtion is printed only each two years of age and if
                 agev[m][i]=agedc[i];       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/       results. So we changed our mind and took the option of the best precision.
            else {    */
               if (andc[i]!=9999){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;    /* If stepm=6 months */
               }    /* nhstepm age range expressed in number of stepm */
             }    agelim=AGESUP;
           }    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
           else if(s[m][i] !=9){ /* Should no more exist */    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    /* if (stepm >= YEARM) hstepm=1;*/
             if(mint[m][i]==99 || anint[m][i]==9999)    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
               agev[m][i]=1;    
             else if(agev[m][i] <agemin){    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               agemin=agev[m][i];    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
             }    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
             else if(agev[m][i] >agemax){    gp=matrix(0,nhstepm,1,nlstate*nlstate);
               agemax=agev[m][i];    gm=matrix(0,nhstepm,1,nlstate*nlstate);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }    for (age=bage; age<=fage; age ++){ 
             /*agev[m][i]=anint[m][i]-annais[i];*/      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
             /*   agev[m][i] = age[i]+2*m;*/      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           }      /* if (stepm >= YEARM) hstepm=1;*/
           else { /* =9 */      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
             agev[m][i]=1;  
             s[m][i]=-1;      /* 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 */
         else /*= 0 Unknown */      
           agev[m][i]=1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       }  
          /* Computing  Variances of health expectancies */
     }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     for (i=1; i<=imx; i++)  {         decrease memory allocation */
       for(m=1; (m<= maxwav); m++){      for(theta=1; theta <=npar; theta++){
         if (s[m][i] > (nlstate+ndeath)) {        for(i=1; i<=npar; i++){ 
           printf("Error: Wrong value in nlstate or ndeath\n");            xp[i] = x[i] + (i==theta ?delti[theta]:0);
           goto end;          xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }        }
       }        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
     }        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
     free_vector(severity,1,maxwav);            for(h=0; h<=nhstepm-1; h++){
     free_imatrix(outcome,1,maxwav+1,1,n);              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     free_vector(moisnais,1,n);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
     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);        for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
                gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
     wav=ivector(1,imx);          }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      }/* End theta */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      
          
     /* Concatenates waves */      for(h=0; h<=nhstepm-1; h++)
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       Tcode=ivector(1,100);      
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;       for(ij=1;ij<=nlstate*nlstate;ij++)
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        for(ji=1;ji<=nlstate*nlstate;ji++)
                varhe[ij][ji][(int)age] =0.;
    codtab=imatrix(1,100,1,10);  
    h=0;       printf("%d|",(int)age);fflush(stdout);
    m=pow(2,cptcoveff);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         for(h=0;h<=nhstepm-1;h++){
    for(k=1;k<=cptcoveff; k++){        for(k=0;k<=nhstepm-1;k++){
      for(i=1; i <=(m/pow(2,k));i++){          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
        for(j=1; j <= ncodemax[k]; j++){          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          for(ij=1;ij<=nlstate*nlstate;ij++)
            h++;            for(ji=1;ji<=nlstate*nlstate;ji++)
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/        }
          }      }
        }  
      }      /* Computing expectancies */
    }      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);      for(i=1; i<=nlstate;i++)
       codtab[1][2]=1;codtab[2][2]=2; */        for(j=1; j<=nlstate;j++)
    /* for(i=1; i <=m ;i++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       for(k=1; k <=cptcovn; k++){            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);            
       }            /* 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]);*/
       printf("\n");  
       }          }
       scanf("%d",i);*/  
          fprintf(ficresstdeij,"%3.0f",age );
    /* Calculates basic frequencies. Computes observed prevalence at single age      for(i=1; i<=nlstate;i++){
        and prints on file fileres'p'. */        eip=0.;
         vip=0.;
            for(j=1; j<=nlstate;j++){
              eip += eij[i][j][(int)age];
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
            }
     /* For Powell, parameters are in a vector p[] starting at p[1]      fprintf(ficresstdeij,"\n");
        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) */      fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
     if(mle==1){        for(j=1; j<=nlstate;j++){
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          cptj= (j-1)*nlstate+i;
     }          for(i2=1; i2<=nlstate;i2++)
                for(j2=1; j2<=nlstate;j2++){
     /*--------- results files --------------*/              cptj2= (j2-1)*nlstate+i2;
     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);              if(cptj2 <= cptj)
                  fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
    jk=1;        }
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fprintf(ficrescveij,"\n");
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");     
    for(i=1,jk=1; i <=nlstate; i++){    }
      for(k=1; k <=(nlstate+ndeath); k++){    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
        if (k != i)    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
          {    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
            printf("%d%d ",i,k);    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
            fprintf(ficres,"%1d%1d ",i,k);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            for(j=1; j <=ncovmodel; j++){    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              printf("%f ",p[jk]);    printf("\n");
              fprintf(ficres,"%f ",p[jk]);    fprintf(ficlog,"\n");
              jk++;  
            }    free_vector(xm,1,npar);
            printf("\n");    free_vector(xp,1,npar);
            fprintf(ficres,"\n");    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
          }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
      }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
    }  }
  if(mle==1){  
     /* Computing hessian and covariance matrix */  /************ Variance ******************/
     ftolhess=ftol; /* Usually correct */  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[])
     hesscov(matcov, p, npar, delti, ftolhess, func);  {
  }    /* Variance of health expectancies */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     printf("# Scales (for hessian or gradient estimation)\n");    /* double **newm;*/
      for(i=1,jk=1; i <=nlstate; i++){    double **dnewm,**doldm;
       for(j=1; j <=nlstate+ndeath; j++){    double **dnewmp,**doldmp;
         if (j!=i) {    int i, j, nhstepm, hstepm, h, nstepm ;
           fprintf(ficres,"%1d%1d",i,j);    int k, cptcode;
           printf("%1d%1d",i,j);    double *xp;
           for(k=1; k<=ncovmodel;k++){    double **gp, **gm;  /* for var eij */
             printf(" %.5e",delti[jk]);    double ***gradg, ***trgradg; /*for var eij */
             fprintf(ficres," %.5e",delti[jk]);    double **gradgp, **trgradgp; /* for var p point j */
             jk++;    double *gpp, *gmp; /* for var p point j */
           }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           printf("\n");    double ***p3mat;
           fprintf(ficres,"\n");    double age,agelim, hf;
         }    double ***mobaverage;
       }    int theta;
      }    char digit[4];
        char digitp[25];
     k=1;  
     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");    char fileresprobmorprev[FILENAMELENGTH];
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");  
     for(i=1;i<=npar;i++){    if(popbased==1){
       /*  if (k>nlstate) k=1;      if(mobilav!=0)
       i1=(i-1)/(ncovmodel*nlstate)+1;        strcpy(digitp,"-populbased-mobilav-");
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      else strcpy(digitp,"-populbased-nomobil-");
       printf("%s%d%d",alph[k],i1,tab[i]);*/    }
       fprintf(ficres,"%3d",i);    else 
       printf("%3d",i);      strcpy(digitp,"-stablbased-");
       for(j=1; j<=i;j++){  
         fprintf(ficres," %.5e",matcov[i][j]);    if (mobilav!=0) {
         printf(" %.5e",matcov[i][j]);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       }      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       fprintf(ficres,"\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       printf("\n");        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       k++;      }
     }    }
      
     while((c=getc(ficpar))=='#' && c!= EOF){    strcpy(fileresprobmorprev,"prmorprev"); 
       ungetc(c,ficpar);    sprintf(digit,"%-d",ij);
       fgets(line, MAXLINE, ficpar);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       puts(line);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       fputs(line,ficparo);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     }    strcat(fileresprobmorprev,fileres);
     ungetc(c,ficpar);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     estepm=0;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     if (estepm==0 || estepm < stepm) estepm=stepm;    }
     if (fage <= 2) {    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       bage = ageminpar;   
       fage = agemaxpar;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     }    pstamp(ficresprobmorprev);
        fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fprintf(ficresprobmorprev," p.%-d SE",j);
        for(i=1; i<=nlstate;i++)
     while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     ungetc(c,ficpar);    }  
     fgets(line, MAXLINE, ficpar);    fprintf(ficresprobmorprev,"\n");
     puts(line);    fprintf(ficgp,"\n# Routine varevsij");
     fputs(line,ficparo);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   }    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   ungetc(c,ficpar);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
    /*   } */
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    pstamp(ficresvij);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
          if(popbased==1)
   while((c=getc(ficpar))=='#' && c!= EOF){      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);
     ungetc(c,ficpar);    else
     fgets(line, MAXLINE, ficpar);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     puts(line);    fprintf(ficresvij,"# Age");
     fputs(line,ficparo);    for(i=1; i<=nlstate;i++)
   }      for(j=1; j<=nlstate;j++)
   ungetc(c,ficpar);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
      fprintf(ficresvij,"\n");
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    xp=vector(1,npar);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
   fscanf(ficpar,"pop_based=%d\n",&popbased);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   fprintf(ficparo,"pop_based=%d\n",popbased);      doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   fprintf(ficres,"pop_based=%d\n",popbased);    
      gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   while((c=getc(ficpar))=='#' && c!= EOF){    gpp=vector(nlstate+1,nlstate+ndeath);
     ungetc(c,ficpar);    gmp=vector(nlstate+1,nlstate+ndeath);
     fgets(line, MAXLINE, ficpar);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     puts(line);    
     fputs(line,ficparo);    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
   ungetc(c,ficpar);    }
     else  hstepm=estepm;   
   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);    /* For example we decided to compute the life expectancy with the smallest unit */
 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);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 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);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
 while((c=getc(ficpar))=='#' && c!= EOF){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     ungetc(c,ficpar);       survival function given by stepm (the optimization length). Unfortunately it
     fgets(line, MAXLINE, ficpar);       means that if the survival funtion is printed every two years of age and if
     puts(line);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     fputs(line,ficparo);       results. So we changed our mind and took the option of the best precision.
   }    */
   ungetc(c,ficpar);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
 /*------------ gnuplot -------------*/      gm=matrix(0,nhstepm,1,nlstate);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);  
    
 /*------------ free_vector  -------------*/      for(theta=1; theta <=npar; theta++){
  chdir(path);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
  free_ivector(wav,1,imx);        }
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);        if (popbased==1) {
  /*free_matrix(covar,1,NCOVMAX,1,n);*/          if(mobilav ==0){
  fclose(ficparo);            for(i=1; i<=nlstate;i++)
  fclose(ficres);              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
 /*--------- index.htm --------*/            for(i=1; i<=nlstate;i++)
               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);          }
         }
      
   /*--------------- Prevalence limit --------------*/        for(j=1; j<= nlstate; j++){
            for(h=0; h<=nhstepm; h++){
   strcpy(filerespl,"pl");            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   strcat(filerespl,fileres);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        }
   }        /* This for computing probability of death (h=1 means
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);           computed over hstepm matrices product = hstepm*stepm months) 
   fprintf(ficrespl,"#Prevalence limit\n");           as a weighted average of prlim.
   fprintf(ficrespl,"#Age ");        */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   fprintf(ficrespl,"\n");          for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
   prlim=matrix(1,nlstate,1,nlstate);        }    
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        /* end probability of death */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   k=0;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   agebase=ageminpar;   
   agelim=agemaxpar;        if (popbased==1) {
   ftolpl=1.e-10;          if(mobilav ==0){
   i1=cptcoveff;            for(i=1; i<=nlstate;i++)
   if (cptcovn < 1){i1=1;}              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   for(cptcov=1;cptcov<=i1;cptcov++){            for(i=1; i<=nlstate;i++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              prlim[i][i]=mobaverage[(int)age][i][ij];
         k=k+1;          }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        }
         fprintf(ficrespl,"\n#******");  
         for(j=1;j<=cptcoveff;j++)        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for(h=0; h<=nhstepm; h++){
         fprintf(ficrespl,"******\n");            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                      gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         for (age=agebase; age<=agelim; age++){          }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        }
           fprintf(ficrespl,"%.0f",age );        /* This for computing probability of death (h=1 means
           for(i=1; i<=nlstate;i++)           computed over hstepm matrices product = hstepm*stepm months) 
           fprintf(ficrespl," %.5f", prlim[i][i]);           as a weighted average of prlim.
           fprintf(ficrespl,"\n");        */
         }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   fclose(ficrespl);        }    
         /* end probability of death */
   /*------------- h Pij x at various ages ------------*/  
          for(j=1; j<= nlstate; j++) /* vareij */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          for(h=0; h<=nhstepm; h++){
   if((ficrespij=fopen(filerespij,"w"))==NULL) {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          }
   }  
   printf("Computing pij: result on file '%s' \n", filerespij);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
            gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   stepsize=(int) (stepm+YEARM-1)/YEARM;        }
   /*if (stepm<=24) stepsize=2;*/  
       } /* End theta */
   agelim=AGESUP;  
   hstepm=stepsize*YEARM; /* Every year of age */      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  
        for(h=0; h<=nhstepm; h++) /* veij */
   k=0;        for(j=1; j<=nlstate;j++)
   for(cptcov=1;cptcov<=i1;cptcov++){          for(theta=1; theta <=npar; theta++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            trgradg[h][j][theta]=gradg[h][theta][j];
       k=k+1;  
         fprintf(ficrespij,"\n#****** ");      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(j=1;j<=cptcoveff;j++)        for(theta=1; theta <=npar; theta++)
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          trgradgp[j][theta]=gradgp[theta][j];
         fprintf(ficrespij,"******\n");    
          
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      for(i=1;i<=nlstate;i++)
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        for(j=1;j<=nlstate;j++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          vareij[i][j][(int)age] =0.;
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for(h=0;h<=nhstepm;h++){
           fprintf(ficrespij,"# Age");        for(k=0;k<=nhstepm;k++){
           for(i=1; i<=nlstate;i++)          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
             for(j=1; j<=nlstate+ndeath;j++)          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
               fprintf(ficrespij," %1d-%1d",i,j);          for(i=1;i<=nlstate;i++)
           fprintf(ficrespij,"\n");            for(j=1;j<=nlstate;j++)
            for (h=0; h<=nhstepm; h++){              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        }
             for(i=1; i<=nlstate;i++)      }
               for(j=1; j<=nlstate+ndeath;j++)    
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      /* pptj */
             fprintf(ficrespij,"\n");      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
              }      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
           fprintf(ficrespij,"\n");        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         }          varppt[j][i]=doldmp[j][i];
     }      /* end ppptj */
   }      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
   fclose(ficrespij);      if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
   /*---------- Forecasting ------------------*/            prlim[i][i]=probs[(int)age][i][ij];
   if((stepm == 1) && (strcmp(model,".")==0)){        }else{ /* mobilav */ 
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          for(i=1; i<=nlstate;i++)
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);            prlim[i][i]=mobaverage[(int)age][i][ij];
   }        }
   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);      /* This for computing probability of death (h=1 means
   }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           as a weighted average of prlim.
       */
   /*---------- Health expectancies and variances ------------*/      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   strcpy(filerest,"t");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   strcat(filerest,fileres);      }    
   if((ficrest=fopen(filerest,"w"))==NULL) {      /* end probability of death */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
   strcpy(filerese,"e");          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   strcat(filerese,fileres);        }
   if((ficreseij=fopen(filerese,"w"))==NULL) {      } 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      fprintf(ficresprobmorprev,"\n");
   }  
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
  strcpy(fileresv,"v");        for(j=1; j<=nlstate;j++){
   strcat(fileresv,fileres);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      fprintf(ficresvij,"\n");
   }      free_matrix(gp,0,nhstepm,1,nlstate);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      free_matrix(gm,0,nhstepm,1,nlstate);
   calagedate=-1;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   k=0;    } /* End age */
   for(cptcov=1;cptcov<=i1;cptcov++){    free_vector(gpp,nlstate+1,nlstate+ndeath);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_vector(gmp,nlstate+1,nlstate+ndeath);
       k=k+1;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       fprintf(ficrest,"\n#****** ");    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       for(j=1;j<=cptcoveff;j++)    fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       fprintf(ficrest,"******\n");    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       fprintf(ficreseij,"\n#****** ");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       for(j=1;j<=cptcoveff;j++)  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
       fprintf(ficreseij,"******\n");    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(ficresvij,"\n#****** ");    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
       for(j=1;j<=cptcoveff;j++)    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(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
       fprintf(ficresvij,"******\n");  */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      free_vector(xp,1,npar);
      free_matrix(doldm,1,nlstate,1,nlstate);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    free_matrix(dnewm,1,nlstate,1,npar);
       oldm=oldms;savm=savms;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
        free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      fclose(ficresprobmorprev);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    fflush(ficgp);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    fflush(fichtm); 
       fprintf(ficrest,"\n");  }  /* end varevsij */
   
       epj=vector(1,nlstate+1);  /************ Variance of prevlim ******************/
       for(age=bage; age <=fage ;age++){  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[])
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  {
         if (popbased==1) {    /* Variance of prevalence limit */
           for(i=1; i<=nlstate;i++)    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
             prlim[i][i]=probs[(int)age][i][k];    double **newm;
         }    double **dnewm,**doldm;
            int i, j, nhstepm, hstepm;
         fprintf(ficrest," %4.0f",age);    int k, cptcode;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    double *xp;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    double *gp, *gm;
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    double **gradg, **trgradg;
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    double age,agelim;
           }    int theta;
           epj[nlstate+1] +=epj[j];    
         }    pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
         for(i=1, vepp=0.;i <=nlstate;i++)    fprintf(ficresvpl,"# Age");
           for(j=1;j <=nlstate;j++)    for(i=1; i<=nlstate;i++)
             vepp += vareij[i][j][(int)age];        fprintf(ficresvpl," %1d-%1d",i,i);
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    fprintf(ficresvpl,"\n");
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    xp=vector(1,npar);
         }    dnewm=matrix(1,nlstate,1,npar);
         fprintf(ficrest,"\n");    doldm=matrix(1,nlstate,1,nlstate);
       }    
     }    hstepm=1*YEARM; /* Every year of age */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
 free_matrix(mint,1,maxwav,1,n);    agelim = AGESUP;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     free_vector(weight,1,n);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   fclose(ficreseij);      if (stepm >= YEARM) hstepm=1;
   fclose(ficresvij);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   fclose(ficrest);      gradg=matrix(1,npar,1,nlstate);
   fclose(ficpar);      gp=vector(1,nlstate);
   free_vector(epj,1,nlstate+1);      gm=vector(1,nlstate);
    
   /*------- Variance limit prevalence------*/        for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
   strcpy(fileresvpl,"vpl");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   strcat(fileresvpl,fileres);        }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        for(i=1;i<=nlstate;i++)
     exit(0);          gp[i] = prlim[i][i];
   }      
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   k=0;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   for(cptcov=1;cptcov<=i1;cptcov++){        for(i=1;i<=nlstate;i++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          gm[i] = prlim[i][i];
       k=k+1;  
       fprintf(ficresvpl,"\n#****** ");        for(i=1;i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++)          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      } /* End theta */
       fprintf(ficresvpl,"******\n");  
            trgradg =matrix(1,nlstate,1,npar);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;      for(j=1; j<=nlstate;j++)
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        for(theta=1; theta <=npar; theta++)
     }          trgradg[j][theta]=gradg[theta][j];
  }  
       for(i=1;i<=nlstate;i++)
   fclose(ficresvpl);        varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   /*---------- End : free ----------------*/      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      for(i=1;i<=nlstate;i++)
          varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      fprintf(ficresvpl,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
          fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      fprintf(ficresvpl,"\n");
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_vector(gp,1,nlstate);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_vector(gm,1,nlstate);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(gradg,1,npar,1,nlstate);
        free_matrix(trgradg,1,nlstate,1,npar);
   free_matrix(matcov,1,npar,1,npar);    } /* End age */
   free_vector(delti,1,npar);  
   free_matrix(agev,1,maxwav,1,imx);    free_vector(xp,1,npar);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   if(erreur >0)  
     printf("End of Imach with error or warning %d\n",erreur);  }
   else   printf("End of Imach\n");  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  /************ Variance of one-step probabilities  ******************/
    void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   /* 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);*/    int i, j=0,  i1, k1, l1, t, tj;
   /*------ End -----------*/    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1, first2;
  end:    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
 #ifdef windows    double **dnewm,**doldm;
   /* chdir(pathcd);*/    double *xp;
 #endif    double *gp, *gm;
  /*system("wgnuplot graph.plt");*/    double **gradg, **trgradg;
  /*system("../gp37mgw/wgnuplot graph.plt");*/    double **mu;
  /*system("cd ../gp37mgw");*/    double age,agelim, cov[NCOVMAX+1];
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
  strcpy(plotcmd,GNUPLOTPROGRAM);    int theta;
  strcat(plotcmd," ");    char fileresprob[FILENAMELENGTH];
  strcat(plotcmd,optionfilegnuplot);    char fileresprobcov[FILENAMELENGTH];
  system(plotcmd);    char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
 #ifdef windows  
   while (z[0] != 'q') {    strcpy(fileresprob,"prob"); 
     /* chdir(path); */    strcat(fileresprob,fileres);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     scanf("%s",z);      printf("Problem with resultfile: %s\n", fileresprob);
     if (z[0] == 'c') system("./imach");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     else if (z[0] == 'e') system(optionfilehtm);    }
     else if (z[0] == 'g') system(plotcmd);    strcpy(fileresprobcov,"probcov"); 
     else if (z[0] == 'q') exit(0);    strcat(fileresprobcov,fileres);
   }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
 #endif      printf("Problem with resultfile: %s\n", fileresprobcov);
 }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    avoid:
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int i1, j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: %s, err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successul, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef OSX
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.41  
changed lines
  Added in v.1.156


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