Diff for /imach/src/imach.c between versions 1.23 and 1.166

version 1.23, 2002/02/22 18:08:30 version 1.166, 2014/12/22 11:40:47
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolate Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.166  2014/12/22 11:40:47  brouard
      *** empty log message ***
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.165  2014/12/16 11:20:36  brouard
   first survey ("cross") where individuals from different ages are    Summary: After compiling on Visual C
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    * imach.c (Module): Merging 1.61 to 1.162
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.164  2014/12/16 10:52:11  brouard
   computed from the time spent in each health state according to a    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    * imach.c (Module): Merging 1.61 to 1.162
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.163  2014/12/16 10:30:11  brouard
   conditional to be observed in state i at the first wave. Therefore    * imach.c (Module): Merging 1.61 to 1.162
   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    Revision 1.162  2014/09/25 11:43:39  brouard
   complex model than "constant and age", you should modify the program    Summary: temporary backup 0.99!
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.1  2014/09/16 11:06:58  brouard
   convergence.    Summary: With some code (wrong) for nlopt
   
   The advantage of this computer programme, compared to a simple    Author:
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.161  2014/09/15 20:41:41  brouard
   intermediate interview, the information is lost, but taken into    Summary: Problem with macro SQR on Intel compiler
   account using an interpolation or extrapolation.    
     Revision 1.160  2014/09/02 09:24:05  brouard
   hPijx is the probability to be observed in state i at age x+h    *** empty log message ***
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.159  2014/09/01 10:34:10  brouard
   states. This elementary transition (by month or quarter trimester,    Summary: WIN32
   semester or year) is model as a multinomial logistic.  The hPx    Author: Brouard
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.158  2014/08/27 17:11:51  brouard
   hPijx.    *** empty log message ***
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.157  2014/08/27 16:26:55  brouard
   of the life expectancies. It also computes the prevalence limits.    Summary: Preparing windows Visual studio version
      Author: Brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    In order to compile on Visual studio, time.h is now correct and time_t
   This software have been partly granted by Euro-REVES, a concerted action    and tm struct should be used. difftime should be used but sometimes I
   from the European Union.    just make the differences in raw time format (time(&now).
   It is copyrighted identically to a GNU software product, ie programme and    Trying to suppress #ifdef LINUX
   software can be distributed freely for non commercial use. Latest version    Add xdg-open for __linux in order to open default browser.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.156  2014/08/25 20:10:10  brouard
      *** empty log message ***
 #include <math.h>  
 #include <stdio.h>    Revision 1.155  2014/08/25 18:32:34  brouard
 #include <stdlib.h>    Summary: New compile, minor changes
 #include <unistd.h>    Author: Brouard
   
 #define MAXLINE 256    Revision 1.154  2014/06/20 17:32:08  brouard
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Summary: Outputs now all graphs of convergence to period prevalence
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.153  2014/06/20 16:45:46  brouard
 #define windows    Summary: If 3 live state, convergence to period prevalence on same graph
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Author: Brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.152  2014/06/18 17:54:09  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.151  2014/06/18 16:43:30  brouard
 #define NINTERVMAX 8    *** empty log message ***
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.150  2014/06/18 16:42:35  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 #define MAXN 20000    Author: brouard
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.149  2014/06/18 15:51:14  brouard
 #define AGEBASE 40    Summary: Some fixes in parameter files errors
     Author: Nicolas Brouard
   
 int erreur; /* Error number */    Revision 1.148  2014/06/17 17:38:48  brouard
 int nvar;    Summary: Nothing new
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Author: Brouard
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Just a new packaging for OS/X version 0.98nS
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.147  2014/06/16 10:33:11  brouard
 int popbased=0;    *** empty log message ***
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.146  2014/06/16 10:20:28  brouard
 int maxwav; /* Maxim number of waves */    Summary: Merge
 int jmin, jmax; /* min, max spacing between 2 waves */    Author: Brouard
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Merge, before building revised version.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.145  2014/06/10 21:23:15  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Summary: Debugging with valgrind
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Author: Nicolas Brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    Lot of changes in order to output the results with some covariates
 FILE *ficreseij;    After the Edimburgh REVES conference 2014, it seems mandatory to
   char filerese[FILENAMELENGTH];    improve the code.
  FILE  *ficresvij;    No more memory valgrind error but a lot has to be done in order to
   char fileresv[FILENAMELENGTH];    continue the work of splitting the code into subroutines.
  FILE  *ficresvpl;    Also, decodemodel has been improved. Tricode is still not
   char fileresvpl[FILENAMELENGTH];    optimal. nbcode should be improved. Documentation has been added in
     the source code.
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.143  2014/01/26 09:45:38  brouard
 #define FTOL 1.0e-10    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   
 #define NRANSI    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define ITMAX 200    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   
 #define TOL 2.0e-4    Revision 1.142  2014/01/26 03:57:36  brouard
     Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.141  2014/01/26 02:42:01  brouard
 #define GOLD 1.618034    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.140  2011/09/02 10:37:54  brouard
     Summary: times.h is ok with mingw32 now.
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.139  2010/06/14 07:50:17  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
      I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.138  2010/04/30 18:19:40  brouard
     *** empty log message ***
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.137  2010/04/29 18:11:38  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Module): Checking covariates for more complex models
     than V1+V2. A lot of change to be done. Unstable.
 int imx;  
 int stepm;    Revision 1.136  2010/04/26 20:30:53  brouard
 /* Stepm, step in month: minimum step interpolation*/    (Module): merging some libgsl code. Fixing computation
     of likelione (using inter/intrapolation if mle = 0) in order to
 int m,nb;    get same likelihood as if mle=1.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Some cleaning of code and comments added.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.135  2009/10/29 15:33:14  brouard
 double dateintmean=0;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
 double *weight;    Revision 1.134  2009/10/29 13:18:53  brouard
 int **s; /* Status */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.133  2009/07/06 10:21:25  brouard
     just nforces
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.132  2009/07/06 08:22:05  brouard
     Many tings
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.131  2009/06/20 16:22:47  brouard
 {    Some dimensions resccaled
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
    l1 = strlen( path );                 /* length of path */    lot of cleaning with variables initialized to 0. Trying to make
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.129  2007/08/31 13:49:27  lievre
 #else    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
    s = strrchr( path, '/' );            /* find last / */  
 #endif    Revision 1.128  2006/06/30 13:02:05  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    (Module): Clarifications on computing e.j
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
       if ( getwd( dirc ) == NULL ) {    imach-114 because nhstepm was no more computed in the age
 #else    loop. Now we define nhstepma in the age loop.
       extern char       *getcwd( );    (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    and then all the health expectancies with variances or standard
 #endif    deviation (needs data from the Hessian matrices) which slows the
          return( GLOCK_ERROR_GETCWD );    computation.
       }    In the future we should be able to stop the program is only health
       strcpy( name, path );             /* we've got it */    expectancies and graph are needed without standard deviations.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.126  2006/04/28 17:23:28  brouard
       l2 = strlen( s );                 /* length of filename */    (Module): Yes the sum of survivors was wrong since
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    imach-114 because nhstepm was no more computed in the age
       strcpy( name, s );                /* save file name */    loop. Now we define nhstepma in the age loop.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Version 0.98h
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.125  2006/04/04 15:20:31  lievre
    l1 = strlen( dirc );                 /* length of directory */    Errors in calculation of health expectancies. Age was not initialized.
 #ifdef windows    Forecasting file added.
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Revision 1.124  2006/03/22 17:13:53  lievre
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Parameters are printed with %lf instead of %f (more numbers after the comma).
 #endif    The log-likelihood is printed in the log file
    s = strrchr( name, '.' );            /* find last / */  
    s++;    Revision 1.123  2006/03/20 10:52:43  brouard
    strcpy(ext,s);                       /* save extension */    * imach.c (Module): <title> changed, corresponds to .htm file
    l1= strlen( name);    name. <head> headers where missing.
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    * imach.c (Module): Weights can have a decimal point as for
    finame[l1-l2]= 0;    English (a comma might work with a correct LC_NUMERIC environment,
    return( 0 );                         /* we're done */    otherwise the weight is truncated).
 }    Modification of warning when the covariates values are not 0 or
     1.
     Version 0.98g
 /******************************************/  
     Revision 1.122  2006/03/20 09:45:41  brouard
 void replace(char *s, char*t)    (Module): Weights can have a decimal point as for
 {    English (a comma might work with a correct LC_NUMERIC environment,
   int i;    otherwise the weight is truncated).
   int lg=20;    Modification of warning when the covariates values are not 0 or
   i=0;    1.
   lg=strlen(t);    Version 0.98g
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.121  2006/03/16 17:45:01  lievre
     if (t[i]== '\\') s[i]='/';    * imach.c (Module): Comments concerning covariates added
   }  
 }    * imach.c (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 int nbocc(char *s, char occ)    not 1 month. Version 0.98f
 {  
   int i,j=0;    Revision 1.120  2006/03/16 15:10:38  lievre
   int lg=20;    (Module): refinements in the computation of lli if
   i=0;    status=-2 in order to have more reliable computation if stepm is
   lg=strlen(s);    not 1 month. Version 0.98f
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;    Revision 1.119  2006/03/15 17:42:26  brouard
   }    (Module): Bug if status = -2, the loglikelihood was
   return j;    computed as likelihood omitting the logarithm. Version O.98e
 }  
     Revision 1.118  2006/03/14 18:20:07  brouard
 void cutv(char *u,char *v, char*t, char occ)    (Module): varevsij Comments added explaining the second
 {    table of variances if popbased=1 .
   int i,lg,j,p=0;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   i=0;    (Module): Function pstamp added
   for(j=0; j<=strlen(t)-1; j++) {    (Module): Version 0.98d
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Revision 1.117  2006/03/14 17:16:22  brouard
     (Module): varevsij Comments added explaining the second
   lg=strlen(t);    table of variances if popbased=1 .
   for(j=0; j<p; j++) {    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (u[j] = t[j]);    (Module): Function pstamp added
   }    (Module): Version 0.98d
      u[p]='\0';  
     Revision 1.116  2006/03/06 10:29:27  brouard
    for(j=0; j<= lg; j++) {    (Module): Variance-covariance wrong links and
     if (j>=(p+1))(v[j-p-1] = t[j]);    varian-covariance of ej. is needed (Saito).
   }  
 }    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
 /********************** nrerror ********************/  
     Revision 1.114  2006/02/26 12:57:58  brouard
 void nrerror(char error_text[])    (Module): Some improvements in processing parameter
 {    filename with strsep.
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.113  2006/02/24 14:20:24  brouard
   exit(1);    (Module): Memory leaks checks with valgrind and:
 }    datafile was not closed, some imatrix were not freed and on matrix
 /*********************** vector *******************/    allocation too.
 double *vector(int nl, int nh)  
 {    Revision 1.112  2006/01/30 09:55:26  brouard
   double *v;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    Revision 1.111  2006/01/25 20:38:18  brouard
   return v-nl+NR_END;    (Module): Lots of cleaning and bugs added (Gompertz)
 }    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.110  2006/01/25 00:51:50  brouard
 {    (Module): Lots of cleaning and bugs added (Gompertz)
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.109  2006/01/24 19:37:15  brouard
     (Module): Comments (lines starting with a #) are allowed in data.
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Revision 1.108  2006/01/19 18:05:42  lievre
 {    Gnuplot problem appeared...
   int *v;    To be fixed
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    Revision 1.107  2006/01/19 16:20:37  brouard
   return v-nl+NR_END;    Test existence of gnuplot in imach path
 }  
     Revision 1.106  2006/01/19 13:24:36  brouard
 /******************free ivector **************************/    Some cleaning and links added in html output
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.105  2006/01/05 20:23:19  lievre
   free((FREE_ARG)(v+nl-NR_END));    *** empty log message ***
 }  
     Revision 1.104  2005/09/30 16:11:43  lievre
 /******************* imatrix *******************************/    (Module): sump fixed, loop imx fixed, and simplifications.
 int **imatrix(long nrl, long nrh, long ncl, long nch)    (Module): If the status is missing at the last wave but we know
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    that the person is alive, then we can code his/her status as -2
 {    (instead of missing=-1 in earlier versions) and his/her
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    contributions to the likelihood is 1 - Prob of dying from last
   int **m;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
      the healthy state at last known wave). Version is 0.98
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Revision 1.103  2005/09/30 15:54:49  lievre
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): sump fixed, loop imx fixed, and simplifications.
   m += NR_END;  
   m -= nrl;    Revision 1.102  2004/09/15 17:31:30  brouard
      Add the possibility to read data file including tab characters.
    
   /* allocate rows and set pointers to them */    Revision 1.101  2004/09/15 10:38:38  brouard
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Fix on curr_time
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.100  2004/07/12 18:29:06  brouard
   m[nrl] -= ncl;    Add version for Mac OS X. Just define UNIX in Makefile
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    Revision 1.99  2004/06/05 08:57:40  brouard
      *** empty log message ***
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.98  2004/05/16 15:05:56  brouard
 }    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
 /****************** free_imatrix *************************/    state at each age, but using a Gompertz model: log u =a + b*age .
 void free_imatrix(m,nrl,nrh,ncl,nch)    This is the basic analysis of mortality and should be done before any
       int **m;    other analysis, in order to test if the mortality estimated from the
       long nch,ncl,nrh,nrl;    cross-longitudinal survey is different from the mortality estimated
      /* free an int matrix allocated by imatrix() */    from other sources like vital statistic data.
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    The same imach parameter file can be used but the option for mle should be -3.
   free((FREE_ARG) (m+nrl-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.
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    The output is very simple: only an estimate of the intercept and of
 {    the slope with 95% confident intervals.
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Current limitations:
     A) Even if you enter covariates, i.e. with the
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   if (!m) nrerror("allocation failure 1 in matrix()");    B) There is no computation of Life Expectancy nor Life Table.
   m += NR_END;  
   m -= nrl;    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    suppressed.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.96  2003/07/15 15:38:55  brouard
   m[nrl] -= ncl;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;    Revision 1.95  2003/07/08 07:54:34  brouard
 }    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 /*************************free matrix ************************/    matrix (cov(a12,c31) instead of numbers.
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {    Revision 1.94  2003/06/27 13:00:02  brouard
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Just cleaning
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 /******************* ma3x *******************************/    exist so I changed back to asctime which exists.
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    (Module): Version 0.96b
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Revision 1.92  2003/06/25 16:30:45  brouard
   double ***m;    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.91  2003/06/25 15:30:29  brouard
   m += NR_END;    * imach.c (Repository): Duplicated warning errors corrected.
   m -= nrl;    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    is stamped in powell.  We created a new html file for the graphs
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    concerning matrix of covariance. It has extension -cov.htm.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    Revision 1.89  2003/06/24 12:30:52  brouard
   m[nrl][ncl] += NR_END;    (Module): Some bugs corrected for windows. Also, when
   m[nrl][ncl] -= nll;    mle=-1 a template is output in file "or"mypar.txt with the design
   for (j=ncl+1; j<=nch; j++)    of the covariance matrix to be input.
     m[nrl][j]=m[nrl][j-1]+nlay;  
      Revision 1.88  2003/06/23 17:54:56  brouard
   for (i=nrl+1; i<=nrh; i++) {    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    Revision 1.87  2003/06/18 12:26:01  brouard
       m[i][j]=m[i][j-1]+nlay;    Version 0.96
   }  
   return m;    Revision 1.86  2003/06/17 20:04:08  brouard
 }    (Module): Change position of html and gnuplot routines and added
     routine fileappend.
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    Revision 1.85  2003/06/17 13:12:43  brouard
 {    * imach.c (Repository): Check when date of death was earlier that
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    current date of interview. It may happen when the death was just
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    prior to the death. In this case, dh was negative and likelihood
   free((FREE_ARG)(m+nrl-NR_END));    was wrong (infinity). We still send an "Error" but patch by
 }    assuming that the date of death was just one stepm after the
     interview.
 /***************** f1dim *************************/    (Repository): Because some people have very long ID (first column)
 extern int ncom;    we changed int to long in num[] and we added a new lvector for
 extern double *pcom,*xicom;    memory allocation. But we also truncated to 8 characters (left
 extern double (*nrfunc)(double []);    truncation)
      (Repository): No more line truncation errors.
 double f1dim(double x)  
 {    Revision 1.84  2003/06/13 21:44:43  brouard
   int j;    * imach.c (Repository): Replace "freqsummary" at a correct
   double f;    place. It differs from routine "prevalence" which may be called
   double *xt;    many times. Probs is memory consuming and must be used with
      parcimony.
   xt=vector(1,ncom);    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);    Revision 1.83  2003/06/10 13:39:11  lievre
   free_vector(xt,1,ncom);    *** empty log message ***
   return f;  
 }    Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  */
 {  /*
   int iter;     Interpolated Markov Chain
   double a,b,d,etemp;  
   double fu,fv,fw,fx;    Short summary of the programme:
   double ftemp;    
   double p,q,r,tol1,tol2,u,v,w,x,xm;    This program computes Healthy Life Expectancies from
   double e=0.0;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
      first survey ("cross") where individuals from different ages are
   a=(ax < cx ? ax : cx);    interviewed on their health status or degree of disability (in the
   b=(ax > cx ? ax : cx);    case of a health survey which is our main interest) -2- at least a
   x=w=v=bx;    second wave of interviews ("longitudinal") which measure each change
   fw=fv=fx=(*f)(x);    (if any) in individual health status.  Health expectancies are
   for (iter=1;iter<=ITMAX;iter++) {    computed from the time spent in each health state according to a
     xm=0.5*(a+b);    model. More health states you consider, more time is necessary to reach the
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    Maximum Likelihood of the parameters involved in the model.  The
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    simplest model is the multinomial logistic model where pij is the
     printf(".");fflush(stdout);    probability to be observed in state j at the second wave
 #ifdef DEBUG    conditional to be observed in state i at the first wave. Therefore
     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);    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    'age' is age and 'sex' is a covariate. If you want to have a more
 #endif    complex model than "constant and age", you should modify the program
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    where the markup *Covariates have to be included here again* invites
       *xmin=x;    you to do it.  More covariates you add, slower the
       return fx;    convergence.
     }  
     ftemp=fu;    The advantage of this computer programme, compared to a simple
     if (fabs(e) > tol1) {    multinomial logistic model, is clear when the delay between waves is not
       r=(x-w)*(fx-fv);    identical for each individual. Also, if a individual missed an
       q=(x-v)*(fx-fw);    intermediate interview, the information is lost, but taken into
       p=(x-v)*q-(x-w)*r;    account using an interpolation or extrapolation.  
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;    hPijx is the probability to be observed in state i at age x+h
       q=fabs(q);    conditional to the observed state i at age x. The delay 'h' can be
       etemp=e;    split into an exact number (nh*stepm) of unobserved intermediate
       e=d;    states. This elementary transition (by month, quarter,
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    semester or year) is modelled as a multinomial logistic.  The hPx
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    matrix is simply the matrix product of nh*stepm elementary matrices
       else {    and the contribution of each individual to the likelihood is simply
         d=p/q;    hPijx.
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)    Also this programme outputs the covariance matrix of the parameters but also
           d=SIGN(tol1,xm-x);    of the life expectancies. It also computes the period (stable) prevalence. 
       }    
     } else {    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
       d=CGOLD*(e=(x >= xm ? a-x : b-x));             Institut national d'études démographiques, Paris.
     }    This software have been partly granted by Euro-REVES, a concerted action
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    from the European Union.
     fu=(*f)(u);    It is copyrighted identically to a GNU software product, ie programme and
     if (fu <= fx) {    software can be distributed freely for non commercial use. Latest version
       if (u >= x) a=x; else b=x;    can be accessed at http://euroreves.ined.fr/imach .
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
         } else {    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
           if (u < x) a=u; else b=u;    
           if (fu <= fw || w == x) {    **********************************************************************/
             v=w;  /*
             w=u;    main
             fv=fw;    read parameterfile
             fw=fu;    read datafile
           } else if (fu <= fv || v == x || v == w) {    concatwav
             v=u;    freqsummary
             fv=fu;    if (mle >= 1)
           }      mlikeli
         }    print results files
   }    if mle==1 
   nrerror("Too many iterations in brent");       computes hessian
   *xmin=x;    read end of parameter file: agemin, agemax, bage, fage, estepm
   return fx;        begin-prev-date,...
 }    open gnuplot file
     open html file
 /****************** mnbrak ***********************/    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
      for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
             double (*func)(double))      freexexit2 possible for memory heap.
 {  
   double ulim,u,r,q, dum;    h Pij x                         | pij_nom  ficrestpij
   double fu;     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
           1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
   *fa=(*func)(*ax);         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   *fb=(*func)(*bx);  
   if (*fb > *fa) {         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
     SHFT(dum,*ax,*bx,dum)         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
       SHFT(dum,*fb,*fa,dum)    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
       }     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   *cx=(*bx)+GOLD*(*bx-*ax);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   *fc=(*func)(*cx);  
   while (*fb > *fc) {    forecasting if prevfcast==1 prevforecast call prevalence()
     r=(*bx-*ax)*(*fb-*fc);    health expectancies
     q=(*bx-*cx)*(*fb-*fa);    Variance-covariance of DFLE
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    prevalence()
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));     movingaverage()
     ulim=(*bx)+GLIMIT*(*cx-*bx);    varevsij() 
     if ((*bx-u)*(u-*cx) > 0.0) {    if popbased==1 varevsij(,popbased)
       fu=(*func)(u);    total life expectancies
     } else if ((*cx-u)*(u-ulim) > 0.0) {    Variance of period (stable) prevalence
       fu=(*func)(u);   end
       if (fu < *fc) {  */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  #define POWELL /* Instead of NLOPT */
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  #include <math.h>
       u=ulim;  #include <stdio.h>
       fu=(*func)(u);  #include <stdlib.h>
     } else {  #include <string.h>
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);  #ifdef _WIN32
     }  #include <io.h>
     SHFT(*ax,*bx,*cx,u)  #else
       SHFT(*fa,*fb,*fc,fu)  #include <unistd.h>
       }  #endif
 }  
   #include <limits.h>
 /*************** linmin ************************/  #include <sys/types.h>
   #include <sys/stat.h>
 int ncom;  #include <errno.h>
 double *pcom,*xicom;  /* extern int errno; */
 double (*nrfunc)(double []);  
    /* #ifdef LINUX */
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  /* #include <time.h> */
 {  /* #include "timeval.h" */
   double brent(double ax, double bx, double cx,  /* #else */
                double (*f)(double), double tol, double *xmin);  /* #include <sys/time.h> */
   double f1dim(double x);  /* #endif */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));  #include <time.h>
   int j;  
   double xx,xmin,bx,ax;  #ifdef GSL
   double fx,fb,fa;  #include <gsl/gsl_errno.h>
    #include <gsl/gsl_multimin.h>
   ncom=n;  #endif
   pcom=vector(1,n);  
   xicom=vector(1,n);  #ifdef NLOPT
   nrfunc=func;  #include <nlopt.h>
   for (j=1;j<=n;j++) {  typedef struct {
     pcom[j]=p[j];    double (* function)(double [] );
     xicom[j]=xi[j];  } myfunc_data ;
   }  #endif
   ax=0.0;  
   xx=1.0;  /* #include <libintl.h> */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* #define _(String) gettext (String) */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  #define GNUPLOTPROGRAM "gnuplot"
   for (j=1;j<=n;j++) {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     xi[j] *= xmin;  #define FILENAMELENGTH 132
     p[j] += xi[j];  
   }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   free_vector(xicom,1,n);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   free_vector(pcom,1,n);  
 }  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
   #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #define NINTERVMAX 8
             double (*func)(double []))  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
 {  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
   void linmin(double p[], double xi[], int n, double *fret,  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
               double (*func)(double []));  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
   int i,ibig,j;  #define MAXN 20000
   double del,t,*pt,*ptt,*xit;  #define YEARM 12. /**< Number of months per year */
   double fp,fptt;  #define AGESUP 130
   double *xits;  #define AGEBASE 40
   pt=vector(1,n);  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
   ptt=vector(1,n);  #ifdef _WIN32
   xit=vector(1,n);  #define DIRSEPARATOR '\\'
   xits=vector(1,n);  #define CHARSEPARATOR "\\"
   *fret=(*func)(p);  #define ODIRSEPARATOR '/'
   for (j=1;j<=n;j++) pt[j]=p[j];  #else
   for (*iter=1;;++(*iter)) {  #define DIRSEPARATOR '/'
     fp=(*fret);  #define CHARSEPARATOR "/"
     ibig=0;  #define ODIRSEPARATOR '\\'
     del=0.0;  #endif
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  /* $Id$ */
       printf(" %d %.12f",i, p[i]);  /* $State$ */
     printf("\n");  
     for (i=1;i<=n;i++) {  char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  char fullversion[]="$Revision$ $Date$"; 
       fptt=(*fret);  char strstart[80];
 #ifdef DEBUG  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       printf("fret=%lf \n",*fret);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 #endif  int nvar=0, nforce=0; /* Number of variables, number of forces */
       printf("%d",i);fflush(stdout);  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
       linmin(p,xit,n,fret,func);  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
       if (fabs(fptt-(*fret)) > del) {  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
         del=fabs(fptt-(*fret));  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
         ibig=i;  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
       }  int cptcovprodnoage=0; /**< Number of covariate products without age */   
 #ifdef DEBUG  int cptcoveff=0; /* Total number of covariates to vary for printing results */
       printf("%d %.12e",i,(*fret));  int cptcov=0; /* Working variable */
       for (j=1;j<=n;j++) {  int npar=NPARMAX;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  int nlstate=2; /* Number of live states */
         printf(" x(%d)=%.12e",j,xit[j]);  int ndeath=1; /* Number of dead states */
       }  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       for(j=1;j<=n;j++)  int popbased=0;
         printf(" p=%.12e",p[j]);  
       printf("\n");  int *wav; /* Number of waves for this individuual 0 is possible */
 #endif  int maxwav=0; /* Maxim number of waves */
     }  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
 #ifdef DEBUG  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       int k[2],l;                     to the likelihood and the sum of weights (done by funcone)*/
       k[0]=1;  int mle=1, weightopt=0;
       k[1]=-1;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       printf("Max: %.12e",(*func)(p));  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       for (j=1;j<=n;j++)  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
         printf(" %.12e",p[j]);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       printf("\n");  int countcallfunc=0;  /* Count the number of calls to func */
       for(l=0;l<=1;l++) {  double jmean=1; /* Mean space between 2 waves */
         for (j=1;j<=n;j++) {  double **matprod2(); /* test */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  double **oldm, **newm, **savm; /* Working pointers to matrices */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
         }  /*FILE *fic ; */ /* Used in readdata only */
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       }  FILE *ficlog, *ficrespow;
 #endif  int globpr=0; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
   long ipmx=0; /* Number of contributions */
       free_vector(xit,1,n);  double sw; /* Sum of weights */
       free_vector(xits,1,n);  char filerespow[FILENAMELENGTH];
       free_vector(ptt,1,n);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       free_vector(pt,1,n);  FILE *ficresilk;
       return;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     }  FILE *ficresprobmorprev;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  FILE *fichtm, *fichtmcov; /* Html File */
     for (j=1;j<=n;j++) {  FILE *ficreseij;
       ptt[j]=2.0*p[j]-pt[j];  char filerese[FILENAMELENGTH];
       xit[j]=p[j]-pt[j];  FILE *ficresstdeij;
       pt[j]=p[j];  char fileresstde[FILENAMELENGTH];
     }  FILE *ficrescveij;
     fptt=(*func)(ptt);  char filerescve[FILENAMELENGTH];
     if (fptt < fp) {  FILE  *ficresvij;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  char fileresv[FILENAMELENGTH];
       if (t < 0.0) {  FILE  *ficresvpl;
         linmin(p,xit,n,fret,func);  char fileresvpl[FILENAMELENGTH];
         for (j=1;j<=n;j++) {  char title[MAXLINE];
           xi[j][ibig]=xi[j][n];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
           xi[j][n]=xit[j];  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
         }  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 #ifdef DEBUG  char command[FILENAMELENGTH];
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int  outcmd=0;
         for(j=1;j<=n;j++)  
           printf(" %.12e",xit[j]);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         printf("\n");  
 #endif  char filelog[FILENAMELENGTH]; /* Log file */
       }  char filerest[FILENAMELENGTH];
     }  char fileregp[FILENAMELENGTH];
   }  char popfile[FILENAMELENGTH];
 }  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 /**** Prevalence limit ****************/  
   /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  /* struct timezone tzp; */
 {  /* extern int gettimeofday(); */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  struct tm tml, *gmtime(), *localtime();
      matrix by transitions matrix until convergence is reached */  
   extern time_t time();
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;  struct tm start_time, end_time, curr_time, last_time, forecast_time;
   double **matprod2();  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
   double **out, cov[NCOVMAX], **pmij();  struct tm tm;
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  char strcurr[80], strfor[80];
   
   for (ii=1;ii<=nlstate+ndeath;ii++)  char *endptr;
     for (j=1;j<=nlstate+ndeath;j++){  long lval;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  double dval;
     }  
   #define NR_END 1
    cov[1]=1.;  #define FREE_ARG char*
    #define FTOL 1.0e-10
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  #define NRANSI 
     newm=savm;  #define ITMAX 200 
     /* Covariates have to be included here again */  
      cov[2]=agefin;  #define TOL 2.0e-4 
    
       for (k=1; k<=cptcovn;k++) {  #define CGOLD 0.3819660 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #define ZEPS 1.0e-10 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       }  
       for (k=1; k<=cptcovage;k++)  #define GOLD 1.618034 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  #define GLIMIT 100.0 
       for (k=1; k<=cptcovprod;k++)  #define TINY 1.0e-20 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
   static double maxarg1,maxarg2;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
     savm=oldm;  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
     oldm=newm;  /* #define mytinydouble 1.0e-16 */
     maxmax=0.;  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
     for(j=1;j<=nlstate;j++){  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
       min=1.;  /* static double dsqrarg; */
       max=0.;  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
       for(i=1; i<=nlstate; i++) {  static double sqrarg;
         sumnew=0;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
         prlim[i][j]= newm[i][j]/(1-sumnew);  int agegomp= AGEGOMP;
         max=FMAX(max,prlim[i][j]);  
         min=FMIN(min,prlim[i][j]);  int imx; 
       }  int stepm=1;
       maxmin=max-min;  /* Stepm, step in month: minimum step interpolation*/
       maxmax=FMAX(maxmax,maxmin);  
     }  int estepm;
     if(maxmax < ftolpl){  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       return prlim;  
     }  int m,nb;
   }  long *num;
 }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 /*************** transition probabilities ***************/  double **pmmij, ***probs;
   double *ageexmed,*agecens;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  double dateintmean=0;
 {  
   double s1, s2;  double *weight;
   /*double t34;*/  int **s; /* Status */
   int i,j,j1, nc, ii, jj;  double *agedc;
   double  **covar; /**< covar[j,i], value of jth covariate for individual i,
     for(i=1; i<= nlstate; i++){                    * covar=matrix(0,NCOVMAX,1,n); 
     for(j=1; j<i;j++){                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  double  idx; 
         /*s2 += param[i][j][nc]*cov[nc];*/  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  int *Ndum; /** Freq of modality (tricode */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  int **codtab; /**< codtab=imatrix(1,100,1,10); */
       }  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
       ps[i][j]=s2;  double *lsurv, *lpop, *tpop;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
     for(j=i+1; j<=nlstate+ndeath;j++){  double ftolhess; /**< Tolerance for computing hessian */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /**************** split *************************/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       }  {
       ps[i][j]=s2;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     }       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   }    */ 
     /*ps[3][2]=1;*/    char  *ss;                            /* pointer */
     int   l1, l2;                         /* length counters */
   for(i=1; i<= nlstate; i++){  
      s1=0;    l1 = strlen(path );                   /* length of path */
     for(j=1; j<i; j++)    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       s1+=exp(ps[i][j]);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     for(j=i+1; j<=nlstate+ndeath; j++)    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       s1+=exp(ps[i][j]);      strcpy( name, path );               /* we got the fullname name because no directory */
     ps[i][i]=1./(s1+1.);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     for(j=1; j<i; j++)        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       ps[i][j]= exp(ps[i][j])*ps[i][i];      /* get current working directory */
     for(j=i+1; j<=nlstate+ndeath; j++)      /*    extern  char* getcwd ( char *buf , int len);*/
       ps[i][j]= exp(ps[i][j])*ps[i][i];      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        return( GLOCK_ERROR_GETCWD );
   } /* end i */      }
       /* got dirc from getcwd*/
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      printf(" DIRC = %s \n",dirc);
     for(jj=1; jj<= nlstate+ndeath; jj++){    } else {                              /* strip direcotry from path */
       ps[ii][jj]=0;      ss++;                               /* after this, the filename */
       ps[ii][ii]=1;      l2 = strlen( ss );                  /* length of filename */
     }      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   }      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      printf(" DIRC2 = %s \n",dirc);
     for(jj=1; jj<= nlstate+ndeath; jj++){    }
      printf("%lf ",ps[ii][jj]);    /* We add a separator at the end of dirc if not exists */
    }    l1 = strlen( dirc );                  /* length of directory */
     printf("\n ");    if( dirc[l1-1] != DIRSEPARATOR ){
     }      dirc[l1] =  DIRSEPARATOR;
     printf("\n ");printf("%lf ",cov[2]);*/      dirc[l1+1] = 0; 
 /*      printf(" DIRC3 = %s \n",dirc);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    }
   goto end;*/    ss = strrchr( name, '.' );            /* find last / */
     return ps;    if (ss >0){
 }      ss++;
       strcpy(ext,ss);                     /* save extension */
 /**************** Product of 2 matrices ******************/      l1= strlen( name);
       l2= strlen(ss)+1;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      strncpy( finame, name, l1-l2);
 {      finame[l1-l2]= 0;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    }
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized    return( 0 );                          /* we're done */
      before: only the contents of out is modified. The function returns  }
      a pointer to pointers identical to out */  
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  /******************************************/
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  void replace_back_to_slash(char *s, char*t)
         out[i][k] +=in[i][j]*b[j][k];  {
     int i;
   return out;    int lg=0;
 }    i=0;
     lg=strlen(t);
     for(i=0; i<= lg; i++) {
 /************* Higher Matrix Product ***************/      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    }
 {  }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  
      duration (i.e. until  char *trimbb(char *out, char *in)
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    char *s;
      (typically every 2 years instead of every month which is too big).    s=out;
      Model is determined by parameters x and covariates have to be    while (*in != '\0'){
      included manually here.      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         in++;
      */      }
       *out++ = *in++;
   int i, j, d, h, k;    }
   double **out, cov[NCOVMAX];    *out='\0';
   double **newm;    return s;
   }
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)  char *cutl(char *blocc, char *alocc, char *in, char occ)
     for (j=1;j<=nlstate+ndeath;j++){  {
       oldm[i][j]=(i==j ? 1.0 : 0.0);    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
       po[i][j][0]=(i==j ? 1.0 : 0.0);       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     }       gives blocc="abcdef2ghi" and alocc="j".
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   for(h=1; h <=nhstepm; h++){    */
     for(d=1; d <=hstepm; d++){    char *s, *t;
       newm=savm;    t=in;s=in;
       /* Covariates have to be included here again */    while ((*in != occ) && (*in != '\0')){
       cov[1]=1.;      *alocc++ = *in++;
       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]]];    if( *in == occ){
       for (k=1; k<=cptcovage;k++)      *(alocc)='\0';
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      s=++in;
       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]]];   
     if (s == t) {/* occ not found */
       *(alocc-(in-s))='\0';
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      in=s;
       /*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,    while ( *in != '\0'){
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      *blocc++ = *in++;
       savm=oldm;    }
       oldm=newm;  
     }    *blocc='\0';
     for(i=1; i<=nlstate+ndeath; i++)    return t;
       for(j=1;j<=nlstate+ndeath;j++) {  }
         po[i][j][h]=newm[i][j];  char *cutv(char *blocc, char *alocc, char *in, char occ)
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  {
          */    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
       }       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   } /* end h */       gives blocc="abcdef2ghi" and alocc="j".
   return po;       If occ is not found blocc is null and alocc is equal to in. Returns alocc
 }    */
     char *s, *t;
     t=in;s=in;
 /*************** log-likelihood *************/    while (*in != '\0'){
 double func( double *x)      while( *in == occ){
 {        *blocc++ = *in++;
   int i, ii, j, k, mi, d, kk;        s=in;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      }
   double **out;      *blocc++ = *in++;
   double sw; /* Sum of weights */    }
   double lli; /* Individual log likelihood */    if (s == t) /* occ not found */
   long ipmx;      *(blocc-(in-s))='\0';
   /*extern weight */    else
   /* We are differentiating ll according to initial status */      *(blocc-(in-s)-1)='\0';
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    in=s;
   /*for(i=1;i<imx;i++)    while ( *in != '\0'){
     printf(" %d\n",s[4][i]);      *alocc++ = *in++;
   */    }
   cov[1]=1.;  
     *alocc='\0';
   for(k=1; k<=nlstate; k++) ll[k]=0.;    return s;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  }
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  
     for(mi=1; mi<= wav[i]-1; mi++){  int nbocc(char *s, char occ)
       for (ii=1;ii<=nlstate+ndeath;ii++)  {
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    int i,j=0;
       for(d=0; d<dh[mi][i]; d++){    int lg=20;
         newm=savm;    i=0;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    lg=strlen(s);
         for (kk=1; kk<=cptcovage;kk++) {    for(i=0; i<= lg; i++) {
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    if  (s[i] == occ ) j++;
         }    }
            return j;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  }
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
         savm=oldm;  /* void cutv(char *u,char *v, char*t, char occ) */
         oldm=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') */
       } /* end mult */  /*      gives u="abcdef2ghi" and v="j" *\/ */
        /*   int i,lg,j,p=0; */
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  /*   i=0; */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  /*   lg=strlen(t); */
       ipmx +=1;  /*   for(j=0; j<=lg-1; j++) { */
       sw += weight[i];  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  /*   } */
     } /* end of wave */  
   } /* end of individual */  /*   for(j=0; j<p; j++) { */
   /*     (u[j] = t[j]); */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  /*   } */
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  /*      u[p]='\0'; */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  
   return -l;  /*    for(j=0; j<= lg; j++) { */
 }  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /*   } */
   /* } */
 /*********** Maximum Likelihood Estimation ***************/  
   #ifdef _WIN32
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  char * strsep(char **pp, const char *delim)
 {  {
   int i,j, iter;    char *p, *q;
   double **xi,*delti;           
   double fret;    if ((p = *pp) == NULL)
   xi=matrix(1,npar,1,npar);      return 0;
   for (i=1;i<=npar;i++)    if ((q = strpbrk (p, delim)) != NULL)
     for (j=1;j<=npar;j++)    {
       xi[i][j]=(i==j ? 1.0 : 0.0);      *pp = q + 1;
   printf("Powell\n");      *q = '\0';
   powell(p,xi,npar,ftol,&iter,&fret,func);    }
     else
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      *pp = 0;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    return p;
   }
 }  #endif
   
 /**** Computes Hessian and covariance matrix ***/  /********************** nrerror ********************/
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  
 {  void nrerror(char error_text[])
   double  **a,**y,*x,pd;  {
   double **hess;    fprintf(stderr,"ERREUR ...\n");
   int i, j,jk;    fprintf(stderr,"%s\n",error_text);
   int *indx;    exit(EXIT_FAILURE);
   }
   double hessii(double p[], double delta, int theta, double delti[]);  /*********************** vector *******************/
   double hessij(double p[], double delti[], int i, int j);  double *vector(int nl, int nh)
   void lubksb(double **a, int npar, int *indx, double b[]) ;  {
   void ludcmp(double **a, int npar, int *indx, double *d) ;    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   hess=matrix(1,npar,1,npar);    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
   printf("\nCalculation of the hessian matrix. Wait...\n");  }
   for (i=1;i<=npar;i++){  
     printf("%d",i);fflush(stdout);  /************************ free vector ******************/
     hess[i][i]=hessii(p,ftolhess,i,delti);  void free_vector(double*v, int nl, int nh)
     /*printf(" %f ",p[i]);*/  {
     /*printf(" %lf ",hess[i][i]);*/    free((FREE_ARG)(v+nl-NR_END));
   }  }
    
   for (i=1;i<=npar;i++) {  /************************ivector *******************************/
     for (j=1;j<=npar;j++)  {  int *ivector(long nl,long nh)
       if (j>i) {  {
         printf(".%d%d",i,j);fflush(stdout);    int *v;
         hess[i][j]=hessij(p,delti,i,j);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         hess[j][i]=hess[i][j];        if (!v) nrerror("allocation failure in ivector");
         /*printf(" %lf ",hess[i][j]);*/    return v-nl+NR_END;
       }  }
     }  
   }  /******************free ivector **************************/
   printf("\n");  void free_ivector(int *v, long nl, long nh)
   {
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    free((FREE_ARG)(v+nl-NR_END));
    }
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);  /************************lvector *******************************/
   x=vector(1,npar);  long *lvector(long nl,long nh)
   indx=ivector(1,npar);  {
   for (i=1;i<=npar;i++)    long *v;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   ludcmp(a,npar,indx,&pd);    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
   for (j=1;j<=npar;j++) {  }
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  /******************free lvector **************************/
     lubksb(a,npar,indx,x);  void free_lvector(long *v, long nl, long nh)
     for (i=1;i<=npar;i++){  {
       matcov[i][j]=x[i];    free((FREE_ARG)(v+nl-NR_END));
     }  }
   }  
   /******************* imatrix *******************************/
   printf("\n#Hessian matrix#\n");  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   for (i=1;i<=npar;i++) {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     for (j=1;j<=npar;j++) {  { 
       printf("%.3e ",hess[i][j]);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     }    int **m; 
     printf("\n");    
   }    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   /* Recompute Inverse */    if (!m) nrerror("allocation failure 1 in matrix()"); 
   for (i=1;i<=npar;i++)    m += NR_END; 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    m -= nrl; 
   ludcmp(a,npar,indx,&pd);    
     
   /*  printf("\n#Hessian matrix recomputed#\n");    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   for (j=1;j<=npar;j++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     for (i=1;i<=npar;i++) x[i]=0;    m[nrl] += NR_END; 
     x[j]=1;    m[nrl] -= ncl; 
     lubksb(a,npar,indx,x);    
     for (i=1;i<=npar;i++){    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       y[i][j]=x[i];    
       printf("%.3e ",y[i][j]);    /* return pointer to array of pointers to rows */ 
     }    return m; 
     printf("\n");  } 
   }  
   */  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
   free_matrix(a,1,npar,1,npar);        int **m;
   free_matrix(y,1,npar,1,npar);        long nch,ncl,nrh,nrl; 
   free_vector(x,1,npar);       /* free an int matrix allocated by imatrix() */ 
   free_ivector(indx,1,npar);  { 
   free_matrix(hess,1,npar,1,npar);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
   } 
 }  
   /******************* matrix *******************************/
 /*************** hessian matrix ****************/  double **matrix(long nrl, long nrh, long ncl, long nch)
 double hessii( double x[], double delta, int theta, double delti[])  {
 {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   int i;    double **m;
   int l=1, lmax=20;  
   double k1,k2;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double p2[NPARMAX+1];    if (!m) nrerror("allocation failure 1 in matrix()");
   double res;    m += NR_END;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    m -= nrl;
   double fx;  
   int k=0,kmax=10;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double l1;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
   fx=func(x);    m[nrl] -= ncl;
   for (i=1;i<=npar;i++) p2[i]=x[i];  
   for(l=0 ; l <=lmax; l++){    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     l1=pow(10,l);    return m;
     delts=delt;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     for(k=1 ; k <kmax; k=k+1){  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
       delt = delta*(l1*k);  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
       p2[theta]=x[theta] +delt;     */
       k1=func(p2)-fx;  }
       p2[theta]=x[theta]-delt;  
       k2=func(p2)-fx;  /*************************free matrix ************************/
       /*res= (k1-2.0*fx+k2)/delt/delt; */  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  {
          free((FREE_ARG)(m[nrl]+ncl-NR_END));
 #ifdef DEBUG    free((FREE_ARG)(m+nrl-NR_END));
       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);  }
 #endif  
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  /******************* ma3x *******************************/
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         k=kmax;  {
       }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    double ***m;
         k=kmax; l=lmax*10.;  
       }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    if (!m) nrerror("allocation failure 1 in matrix()");
         delts=delt;    m += NR_END;
       }    m -= nrl;
     }  
   }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   delti[theta]=delts;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   return res;    m[nrl] += NR_END;
      m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 double hessij( double x[], double delti[], int thetai,int thetaj)  
 {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   int i;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   int l=1, l1, lmax=20;    m[nrl][ncl] += NR_END;
   double k1,k2,k3,k4,res,fx;    m[nrl][ncl] -= nll;
   double p2[NPARMAX+1];    for (j=ncl+1; j<=nch; j++) 
   int k;      m[nrl][j]=m[nrl][j-1]+nlay;
     
   fx=func(x);    for (i=nrl+1; i<=nrh; i++) {
   for (k=1; k<=2; k++) {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     for (i=1;i<=npar;i++) p2[i]=x[i];      for (j=ncl+1; j<=nch; j++) 
     p2[thetai]=x[thetai]+delti[thetai]/k;        m[i][j]=m[i][j-1]+nlay;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    }
     k1=func(p2)-fx;    return m; 
      /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     p2[thetai]=x[thetai]+delti[thetai]/k;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    */
     k2=func(p2)-fx;  }
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  /*************************free ma3x ************************/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     k3=func(p2)-fx;  {
      free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     p2[thetai]=x[thetai]-delti[thetai]/k;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    free((FREE_ARG)(m+nrl-NR_END));
     k4=func(p2)-fx;  }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  
 #ifdef DEBUG  /*************** function subdirf ***********/
     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);  char *subdirf(char fileres[])
 #endif  {
   }    /* Caution optionfilefiname is hidden */
   return res;    strcpy(tmpout,optionfilefiname);
 }    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
 /************** Inverse of matrix **************/    return tmpout;
 void ludcmp(double **a, int n, int *indx, double *d)  }
 {  
   int i,imax,j,k;  /*************** function subdirf2 ***********/
   double big,dum,sum,temp;  char *subdirf2(char fileres[], char *preop)
   double *vv;  {
      
   vv=vector(1,n);    /* Caution optionfilefiname is hidden */
   *d=1.0;    strcpy(tmpout,optionfilefiname);
   for (i=1;i<=n;i++) {    strcat(tmpout,"/");
     big=0.0;    strcat(tmpout,preop);
     for (j=1;j<=n;j++)    strcat(tmpout,fileres);
       if ((temp=fabs(a[i][j])) > big) big=temp;    return tmpout;
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  }
     vv[i]=1.0/big;  
   }  /*************** function subdirf3 ***********/
   for (j=1;j<=n;j++) {  char *subdirf3(char fileres[], char *preop, char *preop2)
     for (i=1;i<j;i++) {  {
       sum=a[i][j];    
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    /* Caution optionfilefiname is hidden */
       a[i][j]=sum;    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/");
     big=0.0;    strcat(tmpout,preop);
     for (i=j;i<=n;i++) {    strcat(tmpout,preop2);
       sum=a[i][j];    strcat(tmpout,fileres);
       for (k=1;k<j;k++)    return tmpout;
         sum -= a[i][k]*a[k][j];  }
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {  char *asc_diff_time(long time_sec, char ascdiff[])
         big=dum;  {
         imax=i;    long sec_left, days, hours, minutes;
       }    days = (time_sec) / (60*60*24);
     }    sec_left = (time_sec) % (60*60*24);
     if (j != imax) {    hours = (sec_left) / (60*60) ;
       for (k=1;k<=n;k++) {    sec_left = (sec_left) %(60*60);
         dum=a[imax][k];    minutes = (sec_left) /60;
         a[imax][k]=a[j][k];    sec_left = (sec_left) % (60);
         a[j][k]=dum;    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
       }    return ascdiff;
       *d = -(*d);  }
       vv[imax]=vv[j];  
     }  /***************** f1dim *************************/
     indx[j]=imax;  extern int ncom; 
     if (a[j][j] == 0.0) a[j][j]=TINY;  extern double *pcom,*xicom;
     if (j != n) {  extern double (*nrfunc)(double []); 
       dum=1.0/(a[j][j]);   
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  double f1dim(double x) 
     }  { 
   }    int j; 
   free_vector(vv,1,n);  /* Doesn't work */    double f;
 ;    double *xt; 
 }   
     xt=vector(1,ncom); 
 void lubksb(double **a, int n, int *indx, double b[])    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 {    f=(*nrfunc)(xt); 
   int i,ii=0,ip,j;    free_vector(xt,1,ncom); 
   double sum;    return f; 
    } 
   for (i=1;i<=n;i++) {  
     ip=indx[i];  /*****************brent *************************/
     sum=b[ip];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     b[ip]=b[i];  { 
     if (ii)    int iter; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    double a,b,d,etemp;
     else if (sum) ii=i;    double fu=0,fv,fw,fx;
     b[i]=sum;    double ftemp=0.;
   }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   for (i=n;i>=1;i--) {    double e=0.0; 
     sum=b[i];   
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    a=(ax < cx ? ax : cx); 
     b[i]=sum/a[i][i];    b=(ax > cx ? ax : cx); 
   }    x=w=v=bx; 
 }    fw=fv=fx=(*f)(x); 
     for (iter=1;iter<=ITMAX;iter++) { 
 /************ Frequencies ********************/      xm=0.5*(a+b); 
 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)      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 {  /* Some frequencies */      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
        printf(".");fflush(stdout);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      fprintf(ficlog,".");fflush(ficlog);
   double ***freq; /* Frequencies */  #ifdef DEBUGBRENT
   double *pp;      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);
   double pos, k2, dateintsum=0,k2cpt=0;      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);
   FILE *ficresp;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   char fileresp[FILENAMELENGTH];  #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   pp=vector(1,nlstate);        *xmin=x; 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        return fx; 
   strcpy(fileresp,"p");      } 
   strcat(fileresp,fileres);      ftemp=fu;
   if((ficresp=fopen(fileresp,"w"))==NULL) {      if (fabs(e) > tol1) { 
     printf("Problem with prevalence resultfile: %s\n", fileresp);        r=(x-w)*(fx-fv); 
     exit(0);        q=(x-v)*(fx-fw); 
   }        p=(x-v)*q-(x-w)*r; 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        q=2.0*(q-r); 
   j1=0;        if (q > 0.0) p = -p; 
         q=fabs(q); 
   j=cptcoveff;        etemp=e; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   for(k1=1; k1<=j;k1++){          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
    for(i1=1; i1<=ncodemax[k1];i1++){        else { 
        j1++;          d=p/q; 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          u=x+d; 
          scanf("%d", i);*/          if (u-a < tol2 || b-u < tol2) 
         for (i=-1; i<=nlstate+ndeath; i++)              d=SIGN(tol1,xm-x); 
          for (jk=-1; jk<=nlstate+ndeath; jk++)          } 
            for(m=agemin; m <= agemax+3; m++)      } else { 
              freq[i][jk][m]=0;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
         dateintsum=0;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         k2cpt=0;      fu=(*f)(u); 
        for (i=1; i<=imx; i++) {      if (fu <= fx) { 
          bool=1;        if (u >= x) a=x; else b=x; 
          if  (cptcovn>0) {        SHFT(v,w,x,u) 
            for (z1=1; z1<=cptcoveff; z1++)          SHFT(fv,fw,fx,fu) 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          } else { 
                bool=0;            if (u < x) a=u; else b=u; 
          }            if (fu <= fw || w == x) { 
          if (bool==1) {              v=w; 
            for(m=firstpass; m<=lastpass; m++){              w=u; 
              k2=anint[m][i]+(mint[m][i]/12.);              fv=fw; 
              if ((k2>=dateprev1) && (k2<=dateprev2)) {              fw=fu; 
                if(agev[m][i]==0) agev[m][i]=agemax+1;            } else if (fu <= fv || v == x || v == w) { 
                if(agev[m][i]==1) agev[m][i]=agemax+2;              v=u; 
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];              fv=fu; 
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            } 
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          } 
                  dateintsum=dateintsum+k2;    } 
                  k2cpt++;    nrerror("Too many iterations in brent"); 
                }    *xmin=x; 
     return fx; 
              }  } 
            }  
          }  /****************** mnbrak ***********************/
        }  
         if  (cptcovn>0) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
          fprintf(ficresp, "\n#********** Variable ");              double (*func)(double)) 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  { 
        fprintf(ficresp, "**********\n#");    double ulim,u,r,q, dum;
         }    double fu; 
        for(i=1; i<=nlstate;i++)   
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    *fa=(*func)(*ax); 
        fprintf(ficresp, "\n");    *fb=(*func)(*bx); 
            if (*fb > *fa) { 
   for(i=(int)agemin; i <= (int)agemax+3; i++){      SHFT(dum,*ax,*bx,dum) 
     if(i==(int)agemax+3)        SHFT(dum,*fb,*fa,dum) 
       printf("Total");        } 
     else    *cx=(*bx)+GOLD*(*bx-*ax); 
       printf("Age %d", i);    *fc=(*func)(*cx); 
     for(jk=1; jk <=nlstate ; jk++){    while (*fb > *fc) { /* Declining fa, fb, fc */
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      r=(*bx-*ax)*(*fb-*fc); 
         pp[jk] += freq[jk][m][i];      q=(*bx-*cx)*(*fb-*fa); 
     }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     for(jk=1; jk <=nlstate ; jk++){        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
       for(m=-1, pos=0; m <=0 ; m++)      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
         pos += freq[jk][m][i];      if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
       if(pp[jk]>=1.e-10)        fu=(*func)(u); 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  #ifdef DEBUG
       else        /* f(x)=A(x-u)**2+f(u) */
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        double A, fparabu; 
     }        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
         fparabu= *fa - A*(*ax-u)*(*ax-u);
      for(jk=1; jk <=nlstate ; jk++){        printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
         pp[jk] += freq[jk][m][i];  #endif 
      }      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
         fu=(*func)(u); 
     for(jk=1,pos=0; jk <=nlstate ; jk++)        if (fu < *fc) { 
       pos += pp[jk];          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     for(jk=1; jk <=nlstate ; jk++){            SHFT(*fb,*fc,fu,(*func)(u)) 
       if(pos>=1.e-5)            } 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
       else        u=ulim; 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        fu=(*func)(u); 
       if( i <= (int) agemax){      } else { 
         if(pos>=1.e-5){        u=(*cx)+GOLD*(*cx-*bx); 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        fu=(*func)(u); 
           probs[i][jk][j1]= pp[jk]/pos;      } 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      SHFT(*ax,*bx,*cx,u) 
         }        SHFT(*fa,*fb,*fc,fu) 
       else        } 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  } 
       }  
     }  /*************** linmin ************************/
     for(jk=-1; jk <=nlstate+ndeath; jk++)  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
       for(m=-1; m <=nlstate+ndeath; m++)  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
     if(i <= (int) agemax)  the value of func at the returned location p . This is actually all accomplished by calling the
       fprintf(ficresp,"\n");  routines mnbrak and brent .*/
     printf("\n");  int ncom; 
     }  double *pcom,*xicom;
     }  double (*nrfunc)(double []); 
  }   
   dateintmean=dateintsum/k2cpt;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
    { 
   fclose(ficresp);    double brent(double ax, double bx, double cx, 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);                 double (*f)(double), double tol, double *xmin); 
   free_vector(pp,1,nlstate);    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   /* End of Freq */                double *fc, double (*func)(double)); 
 }    int j; 
     double xx,xmin,bx,ax; 
 /************ Prevalence ********************/    double fx,fb,fa;
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)   
 {  /* Some frequencies */    ncom=n; 
      pcom=vector(1,n); 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    xicom=vector(1,n); 
   double ***freq; /* Frequencies */    nrfunc=func; 
   double *pp;    for (j=1;j<=n;j++) { 
   double pos, k2;      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
   pp=vector(1,nlstate);    } 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    ax=0.0; 
      xx=1.0; 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
   j1=0;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
    #ifdef DEBUG
   j=cptcoveff;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
    #endif
  for(k1=1; k1<=j;k1++){    for (j=1;j<=n;j++) { 
     for(i1=1; i1<=ncodemax[k1];i1++){      xi[j] *= xmin; 
       j1++;      p[j] += xi[j]; 
      } 
       for (i=-1; i<=nlstate+ndeath; i++)      free_vector(xicom,1,n); 
         for (jk=-1; jk<=nlstate+ndeath; jk++)      free_vector(pcom,1,n); 
           for(m=agemin; m <= agemax+3; m++)  } 
             freq[i][jk][m]=0;  
        
       for (i=1; i<=imx; i++) {  /*************** powell ************************/
         bool=1;  /*
         if  (cptcovn>0) {  Minimization of a function func of n variables. Input consists of an initial starting point
           for (z1=1; z1<=cptcoveff; z1++)  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
               bool=0;  such that failure to decrease by more than this amount on one iteration signals doneness. On
         }  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
         if (bool==1) {  function value at p , and iter is the number of iterations taken. The routine linmin is used.
           for(m=firstpass; m<=lastpass; m++){   */
             k2=anint[m][i]+(mint[m][i]/12.);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {              double (*func)(double [])) 
               if(agev[m][i]==0) agev[m][i]=agemax+1;  { 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    void linmin(double p[], double xi[], int n, double *fret, 
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];                double (*func)(double [])); 
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];      int i,ibig,j; 
             }    double del,t,*pt,*ptt,*xit;
           }    double fp,fptt;
         }    double *xits;
       }    int niterf, itmp;
        
         for(i=(int)agemin; i <= (int)agemax+3; i++){    pt=vector(1,n); 
           for(jk=1; jk <=nlstate ; jk++){    ptt=vector(1,n); 
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    xit=vector(1,n); 
               pp[jk] += freq[jk][m][i];    xits=vector(1,n); 
           }    *fret=(*func)(p); 
           for(jk=1; jk <=nlstate ; jk++){    for (j=1;j<=n;j++) pt[j]=p[j]; 
             for(m=-1, pos=0; m <=0 ; m++)      rcurr_time = time(NULL);  
             pos += freq[jk][m][i];    for (*iter=1;;++(*iter)) { 
         }      fp=(*fret); 
              ibig=0; 
          for(jk=1; jk <=nlstate ; jk++){      del=0.0; 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      rlast_time=rcurr_time;
              pp[jk] += freq[jk][m][i];      /* (void) gettimeofday(&curr_time,&tzp); */
          }      rcurr_time = time(NULL);  
                curr_time = *localtime(&rcurr_time);
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
          for(jk=1; jk <=nlstate ; jk++){            /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
            if( i <= (int) agemax){     for (i=1;i<=n;i++) {
              if(pos>=1.e-5){        printf(" %d %.12f",i, p[i]);
                probs[i][jk][j1]= pp[jk]/pos;        fprintf(ficlog," %d %.12lf",i, p[i]);
              }        fprintf(ficrespow," %.12lf", p[i]);
            }      }
          }      printf("\n");
                fprintf(ficlog,"\n");
         }      fprintf(ficrespow,"\n");fflush(ficrespow);
     }      if(*iter <=3){
   }        tml = *localtime(&rcurr_time);
          strcpy(strcurr,asctime(&tml));
          rforecast_time=rcurr_time; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        itmp = strlen(strcurr);
   free_vector(pp,1,nlstate);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
            strcurr[itmp-1]='\0';
 }  /* End of Freq */        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
         fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
 /************* Waves Concatenation ***************/        for(niterf=10;niterf<=30;niterf+=10){
           rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          forecast_time = *localtime(&rforecast_time);
 {          strcpy(strfor,asctime(&forecast_time));
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          itmp = strlen(strfor);
      Death is a valid wave (if date is known).          if(strfor[itmp-1]=='\n')
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          strfor[itmp-1]='\0';
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
      and mw[mi+1][i]. dh depends on stepm.          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
      */        }
       }
   int i, mi, m;      for (i=1;i<=n;i++) { 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
      double sum=0., jmean=0.;*/        fptt=(*fret); 
   #ifdef DEBUG
   int j, k=0,jk, ju, jl;            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
   double sum=0.;            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
   jmin=1e+5;  #endif
   jmax=-1;        printf("%d",i);fflush(stdout);
   jmean=0.;        fprintf(ficlog,"%d",i);fflush(ficlog);
   for(i=1; i<=imx; i++){        linmin(p,xit,n,fret,func); 
     mi=0;        if (fabs(fptt-(*fret)) > del) { 
     m=firstpass;          del=fabs(fptt-(*fret)); 
     while(s[m][i] <= nlstate){          ibig=i; 
       if(s[m][i]>=1)        } 
         mw[++mi][i]=m;  #ifdef DEBUG
       if(m >=lastpass)        printf("%d %.12e",i,(*fret));
         break;        fprintf(ficlog,"%d %.12e",i,(*fret));
       else        for (j=1;j<=n;j++) {
         m++;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     }/* end while */          printf(" x(%d)=%.12e",j,xit[j]);
     if (s[m][i] > nlstate){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       mi++;     /* Death is another wave */        }
       /* if(mi==0)  never been interviewed correctly before death */        for(j=1;j<=n;j++) {
          /* Only death is a correct wave */          printf(" p(%d)=%.12e",j,p[j]);
       mw[mi][i]=m;          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
     }        }
         printf("\n");
     wav[i]=mi;        fprintf(ficlog,"\n");
     if(mi==0)  #endif
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      } /* end i */
   }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
   for(i=1; i<=imx; i++){        int k[2],l;
     for(mi=1; mi<wav[i];mi++){        k[0]=1;
       if (stepm <=0)        k[1]=-1;
         dh[mi][i]=1;        printf("Max: %.12e",(*func)(p));
       else{        fprintf(ficlog,"Max: %.12e",(*func)(p));
         if (s[mw[mi+1][i]][i] > nlstate) {        for (j=1;j<=n;j++) {
           if (agedc[i] < 2*AGESUP) {          printf(" %.12e",p[j]);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          fprintf(ficlog," %.12e",p[j]);
           if(j==0) j=1;  /* Survives at least one month after exam */        }
           k=k+1;        printf("\n");
           if (j >= jmax) jmax=j;        fprintf(ficlog,"\n");
           if (j <= jmin) jmin=j;        for(l=0;l<=1;l++) {
           sum=sum+j;          for (j=1;j<=n;j++) {
           /* if (j<10) printf("j=%d num=%d ",j,i); */            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]);
         }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         else{          }
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           k=k+1;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           if (j >= jmax) jmax=j;        }
           else if (j <= jmin)jmin=j;  #endif
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  
           sum=sum+j;  
         }        free_vector(xit,1,n); 
         jk= j/stepm;        free_vector(xits,1,n); 
         jl= j -jk*stepm;        free_vector(ptt,1,n); 
         ju= j -(jk+1)*stepm;        free_vector(pt,1,n); 
         if(jl <= -ju)        return; 
           dh[mi][i]=jk;      } 
         else      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
           dh[mi][i]=jk+1;      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
         if(dh[mi][i]==0)        ptt[j]=2.0*p[j]-pt[j]; 
           dh[mi][i]=1; /* At least one step */        xit[j]=p[j]-pt[j]; 
       }        pt[j]=p[j]; 
     }      } 
   }      fptt=(*func)(ptt); 
   jmean=sum/k;      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
  }        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
 /*********** Tricode ****************************/        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
 void tricode(int *Tvar, int **nbcode, int imx)        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
 {        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
   int Ndum[20],ij=1, k, j, i;        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
   int cptcode=0;        /* Thus we compare delta(2h) with observed f1-f3 */
   cptcoveff=0;        /* or best gain on one ancient line 'del' with total  */
          /* gain f1-f2 = f1 - f2 - 'del' with del  */
   for (k=0; k<19; k++) Ndum[k]=0;        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   for (k=1; k<=7; k++) ncodemax[k]=0;  
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        t= t- del*SQR(fp-fptt);
     for (i=1; i<=imx; i++) {        printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
       ij=(int)(covar[Tvar[j]][i]);        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
       Ndum[ij]++;  #ifdef DEBUG
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
       if (ij > cptcode) cptcode=ij;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
     }        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
     for (i=0; i<=cptcode; i++) {        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
       if(Ndum[i]!=0) ncodemax[j]++;        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
     }  #endif
     ij=1;        if (t < 0.0) { /* Then we use it for last direction */
           linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
           for (j=1;j<=n;j++) { 
     for (i=1; i<=ncodemax[j]; i++) {            xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
       for (k=0; k<=19; k++) {            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
         if (Ndum[k] != 0) {          }
           nbcode[Tvar[j]][ij]=k;          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
           ij++;          fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
         }  
         if (ij > ncodemax[j]) break;  #ifdef DEBUG
       }            printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     }          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   }            for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
  for (k=0; k<19; k++) Ndum[k]=0;            fprintf(ficlog," %.12e",xit[j]);
           }
  for (i=1; i<=ncovmodel-2; i++) {          printf("\n");
       ij=Tvar[i];          fprintf(ficlog,"\n");
       Ndum[ij]++;  #endif
     }        } /* end of t negative */
       } /* end if (fptt < fp)  */
  ij=1;    } 
  for (i=1; i<=10; i++) {  } 
    if((Ndum[i]!=0) && (i<=ncov)){  
      Tvaraff[ij]=i;  /**** Prevalence limit (stable or period prevalence)  ****************/
      ij++;  
    }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
  }  {
      /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     cptcoveff=ij-1;       matrix by transitions matrix until convergence is reached */
 }  
     int i, ii,j,k;
 /*********** Health Expectancies ****************/    double min, max, maxmin, maxmax,sumnew=0.;
     /* double **matprod2(); */ /* test */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    double **out, cov[NCOVMAX+1], **pmij();
 {    double **newm;
   /* Health expectancies */    double agefin, delaymax=50 ; /* Max number of years to converge */
   int i, j, nhstepm, hstepm, h;  
   double age, agelim,hf;    for (ii=1;ii<=nlstate+ndeath;ii++)
   double ***p3mat;      for (j=1;j<=nlstate+ndeath;j++){
          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficreseij,"# Health expectancies\n");      }
   fprintf(ficreseij,"# Age");  
   for(i=1; i<=nlstate;i++)     cov[1]=1.;
     for(j=1; j<=nlstate;j++)   
       fprintf(ficreseij," %1d-%1d",i,j);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   fprintf(ficreseij,"\n");    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
   hstepm=1*YEARM; /*  Every j years of age (in month) */      /* Covariates have to be included here again */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      cov[2]=agefin;
       
   agelim=AGESUP;      for (k=1; k<=cptcovn;k++) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     /* nhstepm age range expressed in number of stepm */        /*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]]);*/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);      }
     /* Typically if 20 years = 20*12/6=40 stepm */      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
     if (stepm >= YEARM) hstepm=1;      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
       /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
     for(i=1; i<=nlstate;i++)      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
       for(j=1; j<=nlstate;j++)      
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){      savm=oldm;
           eij[i][j][(int)age] +=p3mat[i][j][h];      oldm=newm;
         }      maxmax=0.;
          for(j=1;j<=nlstate;j++){
     hf=1;        min=1.;
     if (stepm >= YEARM) hf=stepm/YEARM;        max=0.;
     fprintf(ficreseij,"%.0f",age );        for(i=1; i<=nlstate; i++) {
     for(i=1; i<=nlstate;i++)          sumnew=0;
       for(j=1; j<=nlstate;j++){          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          prlim[i][j]= newm[i][j]/(1-sumnew);
       }          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
     fprintf(ficreseij,"\n");          max=FMAX(max,prlim[i][j]);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          min=FMIN(min,prlim[i][j]);
   }        }
 }        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
 /************ Variance ******************/      }
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)      if(maxmax < ftolpl){
 {        return prlim;
   /* Variance of health expectancies */      }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    }
   double **newm;  }
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm, h;  /*************** transition probabilities ***************/ 
   int k, cptcode;  
   double *xp;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   double **gp, **gm;  {
   double ***gradg, ***trgradg;    /* According to parameters values stored in x and the covariate's values stored in cov,
   double ***p3mat;       computes the probability to be observed in state j being in state i by appying the
   double age,agelim;       model to the ncovmodel covariates (including constant and age).
   int theta;       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
        and, according on how parameters are entered, the position of the coefficient xij(nc) of the
    fprintf(ficresvij,"# Covariances of life expectancies\n");       ncth covariate in the global vector x is given by the formula:
   fprintf(ficresvij,"# Age");       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
   for(i=1; i<=nlstate;i++)       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
     for(j=1; j<=nlstate;j++)       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
   fprintf(ficresvij,"\n");       Outputs ps[i][j] the probability to be observed in j being in j according to
        the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   xp=vector(1,npar);    */
   dnewm=matrix(1,nlstate,1,npar);    double s1, lnpijopii;
   doldm=matrix(1,nlstate,1,nlstate);    /*double t34;*/
      int i,j, nc, ii, jj;
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for(i=1; i<= nlstate; i++){
   agelim = AGESUP;        for(j=1; j<i;j++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            /*lnpijopii += param[i][j][nc]*cov[nc];*/
     if (stepm >= YEARM) hstepm=1;            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     gp=matrix(0,nhstepm,1,nlstate);  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     gm=matrix(0,nhstepm,1,nlstate);        }
         for(j=i+1; j<=nlstate+ndeath;j++){
     for(theta=1; theta <=npar; theta++){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       for(i=1; i<=npar; i++){ /* Computes gradient */            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
       }  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         }
       if (popbased==1) {      }
         for(i=1; i<=nlstate;i++)      
           prlim[i][i]=probs[(int)age][i][ij];      for(i=1; i<= nlstate; i++){
       }        s1=0;
              for(j=1; j<i; j++){
       for(j=1; j<= nlstate; j++){          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         for(h=0; h<=nhstepm; h++){          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        for(j=i+1; j<=nlstate+ndeath; j++){
         }          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       }          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
            }
       for(i=1; i<=npar; i++) /* Computes gradient */        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        ps[i][i]=1./(s1+1.);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          /* Computing other pijs */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for(j=1; j<i; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
       if (popbased==1) {        for(j=i+1; j<=nlstate+ndeath; j++)
         for(i=1; i<=nlstate;i++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
           prlim[i][i]=probs[(int)age][i][ij];        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       }      } /* end i */
       
       for(j=1; j<= nlstate; j++){      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         for(h=0; h<=nhstepm; h++){        for(jj=1; jj<= nlstate+ndeath; jj++){
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          ps[ii][jj]=0;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          ps[ii][ii]=1;
         }        }
       }      }
       
       for(j=1; j<= nlstate; j++)      
         for(h=0; h<=nhstepm; h++){      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
         }      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
     } /* End theta */      /*   } */
       /*   printf("\n "); */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      /* } */
       /* printf("\n ");printf("%lf ",cov[2]);*/
     for(h=0; h<=nhstepm; h++)      /*
       for(j=1; j<=nlstate;j++)        for(i=1; i<= npar; i++) printf("%f ",x[i]);
         for(theta=1; theta <=npar; theta++)        goto end;*/
           trgradg[h][j][theta]=gradg[h][theta][j];      return ps;
   }
     for(i=1;i<=nlstate;i++)  
       for(j=1;j<=nlstate;j++)  /**************** Product of 2 matrices ******************/
         vareij[i][j][(int)age] =0.;  
     for(h=0;h<=nhstepm;h++){  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
       for(k=0;k<=nhstepm;k++){  {
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         for(i=1;i<=nlstate;i++)    /* in, b, out are matrice of pointers which should have been initialized 
           for(j=1;j<=nlstate;j++)       before: only the contents of out is modified. The function returns
             vareij[i][j][(int)age] += doldm[i][j];       a pointer to pointers identical to out */
       }    int i, j, k;
     }    for(i=nrl; i<= nrh; i++)
     h=1;      for(k=ncolol; k<=ncoloh; k++){
     if (stepm >= YEARM) h=stepm/YEARM;        out[i][k]=0.;
     fprintf(ficresvij,"%.0f ",age );        for(j=ncl; j<=nch; j++)
     for(i=1; i<=nlstate;i++)          out[i][k] +=in[i][j]*b[j][k];
       for(j=1; j<=nlstate;j++){      }
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    return out;
       }  }
     fprintf(ficresvij,"\n");  
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);  /************* Higher Matrix Product ***************/
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
   } /* End age */    /* Computes the transition matrix starting at age 'age' over 
         'nhstepm*hstepm*stepm' months (i.e. until
   free_vector(xp,1,npar);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   free_matrix(doldm,1,nlstate,1,npar);       nhstepm*hstepm matrices. 
   free_matrix(dnewm,1,nlstate,1,nlstate);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
 }       for the memory).
        Model is determined by parameters x and covariates have to be 
 /************ Variance of prevlim ******************/       included manually here. 
 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 */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    int i, j, d, h, k;
   double **newm;    double **out, cov[NCOVMAX+1];
   double **dnewm,**doldm;    double **newm;
   int i, j, nhstepm, hstepm;  
   int k, cptcode;    /* Hstepm could be zero and should return the unit matrix */
   double *xp;    for (i=1;i<=nlstate+ndeath;i++)
   double *gp, *gm;      for (j=1;j<=nlstate+ndeath;j++){
   double **gradg, **trgradg;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   double age,agelim;        po[i][j][0]=(i==j ? 1.0 : 0.0);
   int theta;      }
        /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    for(h=1; h <=nhstepm; h++){
   fprintf(ficresvpl,"# Age");      for(d=1; d <=hstepm; d++){
   for(i=1; i<=nlstate;i++)        newm=savm;
       fprintf(ficresvpl," %1d-%1d",i,i);        /* Covariates have to be included here again */
   fprintf(ficresvpl,"\n");        cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   xp=vector(1,npar);        for (k=1; k<=cptcovn;k++) 
   dnewm=matrix(1,nlstate,1,npar);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   doldm=matrix(1,nlstate,1,nlstate);        for (k=1; k<=cptcovage;k++)
            cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   hstepm=1*YEARM; /* Every year of age */        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     if (stepm >= YEARM) hstepm=1;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     gradg=matrix(1,npar,1,nlstate);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     gp=vector(1,nlstate);        savm=oldm;
     gm=vector(1,nlstate);        oldm=newm;
       }
     for(theta=1; theta <=npar; theta++){      for(i=1; i<=nlstate+ndeath; i++)
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(j=1;j<=nlstate+ndeath;j++) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          po[i][j][h]=newm[i][j];
       }          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }
       for(i=1;i<=nlstate;i++)      /*printf("h=%d ",h);*/
         gp[i] = prlim[i][i];    } /* end h */
      /*     printf("\n H=%d \n",h); */
       for(i=1; i<=npar; i++) /* Computes gradient */    return po;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)  #ifdef NLOPT
         gm[i] = prlim[i][i];    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
     double fret;
       for(i=1;i<=nlstate;i++)    double *xt;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    int j;
     } /* End theta */    myfunc_data *d2 = (myfunc_data *) pd;
   /* xt = (p1-1); */
     trgradg =matrix(1,nlstate,1,npar);    xt=vector(1,n); 
     for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
     for(j=1; j<=nlstate;j++)  
       for(theta=1; theta <=npar; theta++)    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
         trgradg[j][theta]=gradg[theta][j];    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
     printf("Function = %.12lf ",fret);
     for(i=1;i<=nlstate;i++)    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
       varpl[i][(int)age] =0.;    printf("\n");
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);   free_vector(xt,1,n);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    return fret;
     for(i=1;i<=nlstate;i++)  }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  #endif
   
     fprintf(ficresvpl,"%.0f ",age );  /*************** log-likelihood *************/
     for(i=1; i<=nlstate;i++)  double func( double *x)
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  {
     fprintf(ficresvpl,"\n");    int i, ii, j, k, mi, d, kk;
     free_vector(gp,1,nlstate);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     free_vector(gm,1,nlstate);    double **out;
     free_matrix(gradg,1,npar,1,nlstate);    double sw; /* Sum of weights */
     free_matrix(trgradg,1,nlstate,1,npar);    double lli; /* Individual log likelihood */
   } /* End age */    int s1, s2;
     double bbh, survp;
   free_vector(xp,1,npar);    long ipmx;
   free_matrix(doldm,1,nlstate,1,npar);    /*extern weight */
   free_matrix(dnewm,1,nlstate,1,nlstate);    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 }    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
 /************ Variance of one-step probabilities  ******************/    */
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)  
 {    ++countcallfunc;
   int i, j;  
   int k=0, cptcode;    cov[1]=1.;
   double **dnewm,**doldm;  
   double *xp;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double *gp, *gm;  
   double **gradg, **trgradg;    if(mle==1){
   double age,agelim, cov[NCOVMAX];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int theta;        /* Computes the values of the ncovmodel covariates of the model
   char fileresprob[FILENAMELENGTH];           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
            Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
   strcpy(fileresprob,"prob");           to be observed in j being in i according to the model.
   strcat(fileresprob,fileres);         */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
     printf("Problem with resultfile: %s\n", fileresprob);          cov[2+k]=covar[Tvar[k]][i];
   }        }
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
             is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
            has been calculated etc */
   xp=vector(1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   cov[1]=1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (age=bage; age<=fage; age ++){            }
     cov[2]=age;          for(d=0; d<dh[mi][i]; d++){
     gradg=matrix(1,npar,1,9);            newm=savm;
     trgradg=matrix(1,9,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            for (kk=1; kk<=cptcovage;kk++) {
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
                }
     for(theta=1; theta <=npar; theta++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(i=1; i<=npar; i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            savm=oldm;
                  oldm=newm;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          } /* end mult */
            
       k=0;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       for(i=1; i<= (nlstate+ndeath); i++){          /* But now since version 0.9 we anticipate for bias at large stepm.
         for(j=1; j<=(nlstate+ndeath);j++){           * If stepm is larger than one month (smallest stepm) and if the exact delay 
            k=k+1;           * (in months) between two waves is not a multiple of stepm, we rounded to 
           gp[k]=pmmij[i][j];           * the nearest (and in case of equal distance, to the lowest) interval but now
         }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       }           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
       for(i=1; i<=npar; i++)           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         xp[i] = x[i] - (i==theta ?delti[theta]:0);           * -stepm/2 to stepm/2 .
               * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);           */
       k=0;          s1=s[mw[mi][i]][i];
       for(i=1; i<=(nlstate+ndeath); i++){          s2=s[mw[mi+1][i]][i];
         for(j=1; j<=(nlstate+ndeath);j++){          bbh=(double)bh[mi][i]/(double)stepm; 
           k=k+1;          /* bias bh is positive if real duration
           gm[k]=pmmij[i][j];           * is higher than the multiple of stepm and negative otherwise.
         }           */
       }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
                if( s2 > nlstate){ 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)            /* i.e. if s2 is a death state and if the date of death is known 
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                 then the contribution to the likelihood is the probability to 
     }               die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)               minus probability to die before dh-stepm . 
       for(theta=1; theta <=npar; theta++)               In version up to 0.92 likelihood was computed
       trgradg[j][theta]=gradg[theta][j];          as if date of death was unknown. Death was treated as any other
            health state: the date of the interview describes the actual state
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          and not the date of a change in health state. The former idea was
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          to consider that at each interview the state was recorded
           (healthy, disable or death) and IMaCh was corrected; but when we
      pmij(pmmij,cov,ncovmodel,x,nlstate);          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
      k=0;          contribution is smaller and very dependent of the step unit
      for(i=1; i<=(nlstate+ndeath); i++){          stepm. It is no more the probability to die between last interview
        for(j=1; j<=(nlstate+ndeath);j++){          and month of death but the probability to survive from last
          k=k+1;          interview up to one month before death multiplied by the
          gm[k]=pmmij[i][j];          probability to die within a month. Thanks to Chris
         }          Jackson for correcting this bug.  Former versions increased
      }          mortality artificially. The bad side is that we add another loop
                which slows down the processing. The difference can be up to 10%
      /*printf("\n%d ",(int)age);          lower mortality.
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            */
                    lli=log(out[s1][s2] - savm[s1][s2]);
   
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  
      }*/          } else if  (s2==-2) {
             for (j=1,survp=0. ; j<=nlstate; j++) 
   fprintf(ficresprob,"\n%d ",(int)age);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             /*survp += out[s1][j]; */
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            lli= log(survp);
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          }
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          
   }          else if  (s2==-4) { 
             for (j=3,survp=0. ; j<=nlstate; j++)  
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));            lli= log(survp); 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          } 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
 }          else if  (s2==-5) { 
  free_vector(xp,1,npar);            for (j=1,survp=0. ; j<=2; j++)  
 fclose(ficresprob);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
  exit(0);            lli= log(survp); 
 }          } 
           
 /***********************************************/          else{
 /**************** Main Program *****************/            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 /***********************************************/            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           } 
 int main(int argc, char *argv[])          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 {          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          ipmx +=1;
   double agedeb, agefin,hf;          sw += weight[i];
   double agemin=1.e20, agemax=-1.e20;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
   double fret;      } /* end of individual */
   double **xi,tmp,delta;    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double dum; /* Dummy variable */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double ***p3mat;        for(mi=1; mi<= wav[i]-1; mi++){
   int *indx;          for (ii=1;ii<=nlstate+ndeath;ii++)
   char line[MAXLINE], linepar[MAXLINE];            for (j=1;j<=nlstate+ndeath;j++){
   char title[MAXLINE];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];            }
            for(d=0; d<=dh[mi][i]; d++){
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   char filerest[FILENAMELENGTH];            for (kk=1; kk<=cptcovage;kk++) {
   char fileregp[FILENAMELENGTH];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   char popfile[FILENAMELENGTH];            }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int firstobs=1, lastobs=10;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int sdeb, sfin; /* Status at beginning and end */            savm=oldm;
   int c,  h , cpt,l;            oldm=newm;
   int ju,jl, mi;          } /* end mult */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          s1=s[mw[mi][i]][i];
   int mobilav=0,popforecast=0;          s2=s[mw[mi+1][i]][i];
   int hstepm, nhstepm;          bbh=(double)bh[mi][i]/(double)stepm; 
   int *popage;/*boolprev=0 if date and zero if wave*/          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;          ipmx +=1;
           sw += weight[i];
   double bage, fage, age, agelim, agebase;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double ftolpl=FTOL;        } /* end of wave */
   double **prlim;      } /* end of individual */
   double *severity;    }  else if(mle==3){  /* exponential inter-extrapolation */
   double ***param; /* Matrix of parameters */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double  *p;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double **matcov; /* Matrix of covariance */        for(mi=1; mi<= wav[i]-1; mi++){
   double ***delti3; /* Scale */          for (ii=1;ii<=nlstate+ndeath;ii++)
   double *delti; /* Scale */            for (j=1;j<=nlstate+ndeath;j++){
   double ***eij, ***vareij;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **varpl; /* Variances of prevalence limits by age */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *epj, vepp;            }
   double kk1, kk2;          for(d=0; d<dh[mi][i]; d++){
   double *popeffectif,*popcount;            newm=savm;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double yp,yp1,yp2;            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";            }
   char *alph[]={"a","a","b","c","d","e"}, str[4];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   char z[1]="c", occ;            oldm=newm;
 #include <sys/time.h>          } /* end mult */
 #include <time.h>        
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   /* long total_usecs;          bbh=(double)bh[mi][i]/(double)stepm; 
   struct timeval start_time, end_time;          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 */
            ipmx +=1;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
   printf("\n%s",version);      } /* end of individual */
   if(argc <=1){    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     printf("\nEnter the parameter file name: ");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     scanf("%s",pathtot);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   else{          for (ii=1;ii<=nlstate+ndeath;ii++)
     strcpy(pathtot,argv[1]);            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   /*cygwin_split_path(pathtot,path,optionfile);            }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          for(d=0; d<dh[mi][i]; d++){
   /* cutv(path,optionfile,pathtot,'\\');*/            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);            for (kk=1; kk<=cptcovage;kk++) {
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   chdir(path);            }
   replace(pathc,path);          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /*-------- arguments in the command line --------*/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   strcpy(fileres,"r");            oldm=newm;
   strcat(fileres, optionfilefiname);          } /* end mult */
   strcat(fileres,".txt");    /* Other files have txt extension */        
           s1=s[mw[mi][i]][i];
   /*---------arguments file --------*/          s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {            lli=log(out[s1][s2] - savm[s1][s2]);
     printf("Problem with optionfile %s\n",optionfile);          }else{
     goto end;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   }          }
           ipmx +=1;
   strcpy(filereso,"o");          sw += weight[i];
   strcat(filereso,fileres);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   if((ficparo=fopen(filereso,"w"))==NULL) {  /*      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]); */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;        } /* end of wave */
   }      } /* end of individual */
     }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   /* Reads comments: lines beginning with '#' */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   while((c=getc(ficpar))=='#' && c!= EOF){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     ungetc(c,ficpar);        for(mi=1; mi<= wav[i]-1; mi++){
     fgets(line, MAXLINE, ficpar);          for (ii=1;ii<=nlstate+ndeath;ii++)
     puts(line);            for (j=1;j<=nlstate+ndeath;j++){
     fputs(line,ficparo);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   ungetc(c,ficpar);            }
           for(d=0; d<dh[mi][i]; d++){
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);            newm=savm;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);            for (kk=1; kk<=cptcovage;kk++) {
 while((c=getc(ficpar))=='#' && c!= EOF){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);          
     puts(line);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     fputs(line,ficparo);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
   ungetc(c,ficpar);            oldm=newm;
            } /* end mult */
            
   covar=matrix(0,NCOVMAX,1,n);          s1=s[mw[mi][i]][i];
   cptcovn=0;          s2=s[mw[mi+1][i]][i];
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
   ncovmodel=2+cptcovn;          sw += weight[i];
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
            /*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]);*/
   /* Read guess parameters */        } /* end of wave */
   /* Reads comments: lines beginning with '#' */      } /* end of individual */
   while((c=getc(ficpar))=='#' && c!= EOF){    } /* End of if */
     ungetc(c,ficpar);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     fgets(line, MAXLINE, ficpar);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     puts(line);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     fputs(line,ficparo);    return -l;
   }  }
   ungetc(c,ficpar);  
    /*************** log-likelihood *************/
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  double funcone( double *x)
     for(i=1; i <=nlstate; i++)  {
     for(j=1; j <=nlstate+ndeath-1; j++){    /* Same as likeli but slower because of a lot of printf and if */
       fscanf(ficpar,"%1d%1d",&i1,&j1);    int i, ii, j, k, mi, d, kk;
       fprintf(ficparo,"%1d%1d",i1,j1);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       printf("%1d%1d",i,j);    double **out;
       for(k=1; k<=ncovmodel;k++){    double lli; /* Individual log likelihood */
         fscanf(ficpar," %lf",&param[i][j][k]);    double llt;
         printf(" %lf",param[i][j][k]);    int s1, s2;
         fprintf(ficparo," %lf",param[i][j][k]);    double bbh, survp;
       }    /*extern weight */
       fscanf(ficpar,"\n");    /* We are differentiating ll according to initial status */
       printf("\n");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       fprintf(ficparo,"\n");    /*for(i=1;i<imx;i++) 
     }      printf(" %d\n",s[4][i]);
      */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    cov[1]=1.;
   
   p=param[1][1];    for(k=1; k<=nlstate; k++) ll[k]=0.;
    
   /* Reads comments: lines beginning with '#' */    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   while((c=getc(ficpar))=='#' && c!= EOF){      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     ungetc(c,ficpar);      for(mi=1; mi<= wav[i]-1; mi++){
     fgets(line, MAXLINE, ficpar);        for (ii=1;ii<=nlstate+ndeath;ii++)
     puts(line);          for (j=1;j<=nlstate+ndeath;j++){
     fputs(line,ficparo);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   ungetc(c,ficpar);          }
         for(d=0; d<dh[mi][i]; d++){
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          newm=savm;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(i=1; i <=nlstate; i++){          for (kk=1; kk<=cptcovage;kk++) {
     for(j=1; j <=nlstate+ndeath-1; j++){            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       fscanf(ficpar,"%1d%1d",&i1,&j1);          }
       printf("%1d%1d",i,j);          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
       fprintf(ficparo,"%1d%1d",i1,j1);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(k=1; k<=ncovmodel;k++){                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         fscanf(ficpar,"%le",&delti3[i][j][k]);          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
         printf(" %le",delti3[i][j][k]);          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
         fprintf(ficparo," %le",delti3[i][j][k]);          savm=oldm;
       }          oldm=newm;
       fscanf(ficpar,"\n");        } /* end mult */
       printf("\n");        
       fprintf(ficparo,"\n");        s1=s[mw[mi][i]][i];
     }        s2=s[mw[mi+1][i]][i];
   }        bbh=(double)bh[mi][i]/(double)stepm; 
   delti=delti3[1][1];        /* bias is positive if real duration
           * is higher than the multiple of stepm and negative otherwise.
   /* Reads comments: lines beginning with '#' */         */
   while((c=getc(ficpar))=='#' && c!= EOF){        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     ungetc(c,ficpar);          lli=log(out[s1][s2] - savm[s1][s2]);
     fgets(line, MAXLINE, ficpar);        } else if  (s2==-2) {
     puts(line);          for (j=1,survp=0. ; j<=nlstate; j++) 
     fputs(line,ficparo);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   }          lli= log(survp);
   ungetc(c,ficpar);        }else if (mle==1){
            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   matcov=matrix(1,npar,1,npar);        } else if(mle==2){
   for(i=1; i <=npar; 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 */
     fscanf(ficpar,"%s",&str);        } else if(mle==3){  /* exponential inter-extrapolation */
     printf("%s",str);          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 */
     fprintf(ficparo,"%s",str);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     for(j=1; j <=i; j++){          lli=log(out[s1][s2]); /* Original formula */
       fscanf(ficpar," %le",&matcov[i][j]);        } else{  /* mle=0 back to 1 */
       printf(" %.5le",matcov[i][j]);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       fprintf(ficparo," %.5le",matcov[i][j]);          /*lli=log(out[s1][s2]); */ /* Original formula */
     }        } /* End of if */
     fscanf(ficpar,"\n");        ipmx +=1;
     printf("\n");        sw += weight[i];
     fprintf(ficparo,"\n");        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   for(i=1; i <=npar; i++)        if(globpr){
     for(j=i+1;j<=npar;j++)          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
       matcov[i][j]=matcov[j][i];   %11.6f %11.6f %11.6f ", \
                      num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   printf("\n");                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
     /*-------- data file ----------*/            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     if((ficres =fopen(fileres,"w"))==NULL) {          }
       printf("Problem with resultfile: %s\n", fileres);goto end;          fprintf(ficresilk," %10.6f\n", -llt);
     }        }
     fprintf(ficres,"#%s\n",version);      } /* end of wave */
        } /* end of individual */
     if((fic=fopen(datafile,"r"))==NULL)    {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       printf("Problem with datafile: %s\n", datafile);goto end;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(globpr==0){ /* First time we count the contributions and weights */
     n= lastobs;      gipmx=ipmx;
     severity = vector(1,maxwav);      gsw=sw;
     outcome=imatrix(1,maxwav+1,1,n);    }
     num=ivector(1,n);    return -l;
     moisnais=vector(1,n);  }
     annais=vector(1,n);  
     moisdc=vector(1,n);  
     andc=vector(1,n);  /*************** function likelione ***********/
     agedc=vector(1,n);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     cod=ivector(1,n);  {
     weight=vector(1,n);    /* This routine should help understanding what is done with 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */       the selection of individuals/waves and
     mint=matrix(1,maxwav,1,n);       to check the exact contribution to the likelihood.
     anint=matrix(1,maxwav,1,n);       Plotting could be done.
     s=imatrix(1,maxwav+1,1,n);     */
     adl=imatrix(1,maxwav+1,1,n);        int k;
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
     i=1;      strcat(fileresilk,fileres);
     while (fgets(line, MAXLINE, fic) != NULL)    {      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       if ((i >= firstobs) && (i <=lastobs)) {        printf("Problem with resultfile: %s\n", fileresilk);
                fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         for (j=maxwav;j>=1;j--){      }
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      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");
           strcpy(line,stra);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      for(k=1; k<=nlstate; k++) 
         }        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
              fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
     *fretone=(*funcone)(p);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    if(*globpri !=0){
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      fflush(fichtm); 
         for (j=ncov;j>=1;j--){    } 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    return;
         }  }
         num[i]=atol(stra);  
          
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  /*********** Maximum Likelihood Estimation ***************/
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         i=i+1;  {
       }    int i,j, iter=0;
     }    double **xi;
     /* printf("ii=%d", ij);    double fret;
        scanf("%d",i);*/    double fretone; /* Only one call to likelihood */
   imx=i-1; /* Number of individuals */    /*  char filerespow[FILENAMELENGTH];*/
   
   /* for (i=1; i<=imx; i++){  #ifdef NLOPT
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    int creturn;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    nlopt_opt opt;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     }    double *lb;
     double minf; /* the minimum objective value, upon return */
     for (i=1; i<=imx; i++)    double * p1; /* Shifted parameters from 0 instead of 1 */
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/    myfunc_data dinst, *d = &dinst;
   #endif
   /* Calculation of the number of parameter from char model*/  
   Tvar=ivector(1,15);  
   Tprod=ivector(1,15);    xi=matrix(1,npar,1,npar);
   Tvaraff=ivector(1,15);    for (i=1;i<=npar;i++)
   Tvard=imatrix(1,15,1,2);      for (j=1;j<=npar;j++)
   Tage=ivector(1,15);              xi[i][j]=(i==j ? 1.0 : 0.0);
        printf("Powell\n");  fprintf(ficlog,"Powell\n");
   if (strlen(model) >1){    strcpy(filerespow,"pow"); 
     j=0, j1=0, k1=1, k2=1;    strcat(filerespow,fileres);
     j=nbocc(model,'+');    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     j1=nbocc(model,'*');      printf("Problem with resultfile: %s\n", filerespow);
     cptcovn=j+1;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     cptcovprod=j1;    }
        fprintf(ficrespow,"# Powell\n# iter -2*LL");
        for (i=1;i<=nlstate;i++)
     strcpy(modelsav,model);      for(j=1;j<=nlstate+ndeath;j++)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       printf("Error. Non available option model=%s ",model);    fprintf(ficrespow,"\n");
       goto end;  #ifdef POWELL
     }    powell(p,xi,npar,ftol,&iter,&fret,func);
      #endif
     for(i=(j+1); i>=1;i--){  
       cutv(stra,strb,modelsav,'+');  #ifdef NLOPT
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  #ifdef NEWUOA
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
       /*scanf("%d",i);*/  #else
       if (strchr(strb,'*')) {    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
         cutv(strd,strc,strb,'*');  #endif
         if (strcmp(strc,"age")==0) {    lb=vector(0,npar-1);
           cptcovprod--;    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
           cutv(strb,stre,strd,'V');    nlopt_set_lower_bounds(opt, lb);
           Tvar[i]=atoi(stre);    nlopt_set_initial_step1(opt, 0.1);
           cptcovage++;    
             Tage[cptcovage]=i;    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
             /*printf("stre=%s ", stre);*/    d->function = func;
         }    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
         else if (strcmp(strd,"age")==0) {    nlopt_set_min_objective(opt, myfunc, d);
           cptcovprod--;    nlopt_set_xtol_rel(opt, ftol);
           cutv(strb,stre,strc,'V');    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
           Tvar[i]=atoi(stre);      printf("nlopt failed! %d\n",creturn); 
           cptcovage++;    }
           Tage[cptcovage]=i;    else {
         }      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
         else {      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
           cutv(strb,stre,strc,'V');      iter=1; /* not equal */
           Tvar[i]=ncov+k1;    }
           cutv(strb,strc,strd,'V');    nlopt_destroy(opt);
           Tprod[k1]=i;  #endif
           Tvard[k1][1]=atoi(strc);    free_matrix(xi,1,npar,1,npar);
           Tvard[k1][2]=atoi(stre);    fclose(ficrespow);
           Tvar[cptcovn+k2]=Tvard[k1][1];    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
           for (k=1; k<=lastobs;k++)    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
           k1++;  }
           k2=k2+2;  
         }  /**** Computes Hessian and covariance matrix ***/
       }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       else {  {
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    double  **a,**y,*x,pd;
        /*  scanf("%d",i);*/    double **hess;
       cutv(strd,strc,strb,'V');    int i, j;
       Tvar[i]=atoi(strc);    int *indx;
       }  
       strcpy(modelsav,stra);      double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
         scanf("%d",i);*/    void lubksb(double **a, int npar, int *indx, double b[]) ;
     }    void ludcmp(double **a, int npar, int *indx, double *d) ;
 }    double gompertz(double p[]);
      hess=matrix(1,npar,1,npar);
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  
   printf("cptcovprod=%d ", cptcovprod);    printf("\nCalculation of the hessian matrix. Wait...\n");
   scanf("%d ",i);*/    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     fclose(fic);    for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
     /*  if(mle==1){*/      fprintf(ficlog,"%d",i);fflush(ficlog);
     if (weightopt != 1) { /* Maximisation without weights*/     
       for(i=1;i<=n;i++) weight[i]=1.0;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     }      
     /*-calculation of age at interview from date of interview and age at death -*/      /*  printf(" %f ",p[i]);
     agev=matrix(1,maxwav,1,imx);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }
    for (i=1; i<=imx; i++)    
      for(m=2; (m<= maxwav); m++)    for (i=1;i<=npar;i++) {
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      for (j=1;j<=npar;j++)  {
          anint[m][i]=9999;        if (j>i) { 
          s[m][i]=-1;          printf(".%d%d",i,j);fflush(stdout);
        }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
              hess[i][j]=hessij(p,delti,i,j,func,npar);
     for (i=1; i<=imx; i++)  {          
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          hess[j][i]=hess[i][j];    
       for(m=1; (m<= maxwav); m++){          /*printf(" %lf ",hess[i][j]);*/
         if(s[m][i] >0){        }
           if (s[m][i] == nlstate+1) {      }
             if(agedc[i]>0)    }
               if(moisdc[i]!=99 && andc[i]!=9999)    printf("\n");
               agev[m][i]=agedc[i];    fprintf(ficlog,"\n");
             else {  
               if (andc[i]!=9999){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
               agev[m][i]=-1;    
               }    a=matrix(1,npar,1,npar);
             }    y=matrix(1,npar,1,npar);
           }    x=vector(1,npar);
           else if(s[m][i] !=9){ /* Should no more exist */    indx=ivector(1,npar);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    for (i=1;i<=npar;i++)
             if(mint[m][i]==99 || anint[m][i]==9999)      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
               agev[m][i]=1;    ludcmp(a,npar,indx,&pd);
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];    for (j=1;j<=npar;j++) {
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      for (i=1;i<=npar;i++) x[i]=0;
             }      x[j]=1;
             else if(agev[m][i] >agemax){      lubksb(a,npar,indx,x);
               agemax=agev[m][i];      for (i=1;i<=npar;i++){ 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        matcov[i][j]=x[i];
             }      }
             /*agev[m][i]=anint[m][i]-annais[i];*/    }
             /*   agev[m][i] = age[i]+2*m;*/  
           }    printf("\n#Hessian matrix#\n");
           else { /* =9 */    fprintf(ficlog,"\n#Hessian matrix#\n");
             agev[m][i]=1;    for (i=1;i<=npar;i++) { 
             s[m][i]=-1;      for (j=1;j<=npar;j++) { 
           }        printf("%.3e ",hess[i][j]);
         }        fprintf(ficlog,"%.3e ",hess[i][j]);
         else /*= 0 Unknown */      }
           agev[m][i]=1;      printf("\n");
       }      fprintf(ficlog,"\n");
        }
     }  
     for (i=1; i<=imx; i++)  {    /* Recompute Inverse */
       for(m=1; (m<= maxwav); m++){    for (i=1;i<=npar;i++)
         if (s[m][i] > (nlstate+ndeath)) {      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
           printf("Error: Wrong value in nlstate or ndeath\n");      ludcmp(a,npar,indx,&pd);
           goto end;  
         }    /*  printf("\n#Hessian matrix recomputed#\n");
       }  
     }    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      x[j]=1;
       lubksb(a,npar,indx,x);
     free_vector(severity,1,maxwav);      for (i=1;i<=npar;i++){ 
     free_imatrix(outcome,1,maxwav+1,1,n);        y[i][j]=x[i];
     free_vector(moisnais,1,n);        printf("%.3e ",y[i][j]);
     free_vector(annais,1,n);        fprintf(ficlog,"%.3e ",y[i][j]);
     /* free_matrix(mint,1,maxwav,1,n);      }
        free_matrix(anint,1,maxwav,1,n);*/      printf("\n");
     free_vector(moisdc,1,n);      fprintf(ficlog,"\n");
     free_vector(andc,1,n);    }
     */
      
     wav=ivector(1,imx);    free_matrix(a,1,npar,1,npar);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    free_matrix(y,1,npar,1,npar);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    free_vector(x,1,npar);
        free_ivector(indx,1,npar);
     /* Concatenates waves */    free_matrix(hess,1,npar,1,npar);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
   
   }
       Tcode=ivector(1,100);  
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  /*************** hessian matrix ****************/
       ncodemax[1]=1;  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  {
          int i;
    codtab=imatrix(1,100,1,10);    int l=1, lmax=20;
    h=0;    double k1,k2;
    m=pow(2,cptcoveff);    double p2[MAXPARM+1]; /* identical to x */
      double res;
    for(k=1;k<=cptcoveff; k++){    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
      for(i=1; i <=(m/pow(2,k));i++){    double fx;
        for(j=1; j <= ncodemax[k]; j++){    int k=0,kmax=10;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    double l1;
            h++;  
            if (h>m) h=1;codtab[h][k]=j;    fx=func(x);
          }    for (i=1;i<=npar;i++) p2[i]=x[i];
        }    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
      }      l1=pow(10,l);
    }      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
    /*for(i=1; i <=m ;i++){        p2[theta]=x[theta] +delt;
      for(k=1; k <=cptcovn; k++){        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);        p2[theta]=x[theta]-delt;
      }        k2=func(p2)-fx;
      printf("\n");        /*res= (k1-2.0*fx+k2)/delt/delt; */
    }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
    scanf("%d",i);*/        
      #ifdef DEBUGHESS
    /* Calculates basic frequencies. Computes observed prevalence at single age        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);
        and prints on file fileres'p'. */        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
            /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
            if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          k=kmax;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          k=kmax; l=lmax*10;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        }
              else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     /* For Powell, parameters are in a vector p[] starting at p[1]          delts=delt;
        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) */      }
     }
     if(mle==1){    delti[theta]=delts;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    return res; 
     }    
      }
     /*--------- results files --------------*/  
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
    {
     int i;
    jk=1;    int l=1, lmax=20;
    fprintf(ficres,"# Parameters\n");    double k1,k2,k3,k4,res,fx;
    printf("# Parameters\n");    double p2[MAXPARM+1];
    for(i=1,jk=1; i <=nlstate; i++){    int k;
      for(k=1; k <=(nlstate+ndeath); k++){  
        if (k != i)    fx=func(x);
          {    for (k=1; k<=2; k++) {
            printf("%d%d ",i,k);      for (i=1;i<=npar;i++) p2[i]=x[i];
            fprintf(ficres,"%1d%1d ",i,k);      p2[thetai]=x[thetai]+delti[thetai]/k;
            for(j=1; j <=ncovmodel; j++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
              printf("%f ",p[jk]);      k1=func(p2)-fx;
              fprintf(ficres,"%f ",p[jk]);    
              jk++;      p2[thetai]=x[thetai]+delti[thetai]/k;
            }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
            printf("\n");      k2=func(p2)-fx;
            fprintf(ficres,"\n");    
          }      p2[thetai]=x[thetai]-delti[thetai]/k;
      }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
    }      k3=func(p2)-fx;
  if(mle==1){    
     /* Computing hessian and covariance matrix */      p2[thetai]=x[thetai]-delti[thetai]/k;
     ftolhess=ftol; /* Usually correct */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     hesscov(matcov, p, npar, delti, ftolhess, func);      k4=func(p2)-fx;
  }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     fprintf(ficres,"# Scales\n");  #ifdef DEBUG
     printf("# Scales\n");      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
      for(i=1,jk=1; i <=nlstate; i++){      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       for(j=1; j <=nlstate+ndeath; j++){  #endif
         if (j!=i) {    }
           fprintf(ficres,"%1d%1d",i,j);    return res;
           printf("%1d%1d",i,j);  }
           for(k=1; k<=ncovmodel;k++){  
             printf(" %.5e",delti[jk]);  /************** Inverse of matrix **************/
             fprintf(ficres," %.5e",delti[jk]);  void ludcmp(double **a, int n, int *indx, double *d) 
             jk++;  { 
           }    int i,imax,j,k; 
           printf("\n");    double big,dum,sum,temp; 
           fprintf(ficres,"\n");    double *vv; 
         }   
       }    vv=vector(1,n); 
      }    *d=1.0; 
        for (i=1;i<=n;i++) { 
     k=1;      big=0.0; 
     fprintf(ficres,"# Covariance\n");      for (j=1;j<=n;j++) 
     printf("# Covariance\n");        if ((temp=fabs(a[i][j])) > big) big=temp; 
     for(i=1;i<=npar;i++){      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       /*  if (k>nlstate) k=1;      vv[i]=1.0/big; 
       i1=(i-1)/(ncovmodel*nlstate)+1;    } 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    for (j=1;j<=n;j++) { 
       printf("%s%d%d",alph[k],i1,tab[i]);*/      for (i=1;i<j;i++) { 
       fprintf(ficres,"%3d",i);        sum=a[i][j]; 
       printf("%3d",i);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       for(j=1; j<=i;j++){        a[i][j]=sum; 
         fprintf(ficres," %.5e",matcov[i][j]);      } 
         printf(" %.5e",matcov[i][j]);      big=0.0; 
       }      for (i=j;i<=n;i++) { 
       fprintf(ficres,"\n");        sum=a[i][j]; 
       printf("\n");        for (k=1;k<j;k++) 
       k++;          sum -= a[i][k]*a[k][j]; 
     }        a[i][j]=sum; 
            if ( (dum=vv[i]*fabs(sum)) >= big) { 
     while((c=getc(ficpar))=='#' && c!= EOF){          big=dum; 
       ungetc(c,ficpar);          imax=i; 
       fgets(line, MAXLINE, ficpar);        } 
       puts(line);      } 
       fputs(line,ficparo);      if (j != imax) { 
     }        for (k=1;k<=n;k++) { 
     ungetc(c,ficpar);          dum=a[imax][k]; 
            a[imax][k]=a[j][k]; 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          a[j][k]=dum; 
            } 
     if (fage <= 2) {        *d = -(*d); 
       bage = agemin;        vv[imax]=vv[j]; 
       fage = agemax;      } 
     }      indx[j]=imax; 
          if (a[j][j] == 0.0) a[j][j]=TINY; 
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      if (j != n) { 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        dum=1.0/(a[j][j]); 
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
        } 
     while((c=getc(ficpar))=='#' && c!= EOF){    } 
     ungetc(c,ficpar);    free_vector(vv,1,n);  /* Doesn't work */
     fgets(line, MAXLINE, ficpar);  ;
     puts(line);  } 
     fputs(line,ficparo);  
   }  void lubksb(double **a, int n, int *indx, double b[]) 
   ungetc(c,ficpar);  { 
      int i,ii=0,ip,j; 
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);    double sum; 
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);   
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    for (i=1;i<=n;i++) { 
            ip=indx[i]; 
   while((c=getc(ficpar))=='#' && c!= EOF){      sum=b[ip]; 
     ungetc(c,ficpar);      b[ip]=b[i]; 
     fgets(line, MAXLINE, ficpar);      if (ii) 
     puts(line);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     fputs(line,ficparo);      else if (sum) ii=i; 
   }      b[i]=sum; 
   ungetc(c,ficpar);    } 
      for (i=n;i>=1;i--) { 
       sum=b[i]; 
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      b[i]=sum/a[i][i]; 
     } 
   fscanf(ficpar,"pop_based=%d\n",&popbased);  } 
    fprintf(ficparo,"pop_based=%d\n",popbased);    
    fprintf(ficres,"pop_based=%d\n",popbased);    void pstamp(FILE *fichier)
   {
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     ungetc(c,ficpar);  }
     fgets(line, MAXLINE, ficpar);  
     puts(line);  /************ Frequencies ********************/
     fputs(line,ficparo);  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 */
   ungetc(c,ficpar);    
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);    int i, m, jk, j1, bool, z1,j;
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    int first;
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    double ***freq; /* Frequencies */
     double *pp, **prop;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     char fileresp[FILENAMELENGTH];
        
     /*------------ gnuplot -------------*/    pp=vector(1,nlstate);
     /*chdir(pathcd);*/    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(optionfilegnuplot,optionfilefiname);    strcpy(fileresp,"p");
     strcat(optionfilegnuplot,".plt");    strcat(fileresp,fileres);
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);goto end;      printf("Problem with prevalence resultfile: %s\n", fileresp);
     }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 #ifdef windows      exit(0);
     fprintf(ficgp,"cd \"%s\" \n",pathc);    }
 #endif    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
 m=pow(2,cptcoveff);    j1=0;
      
  /* 1eme*/    j=cptcoveff;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    for (k1=1; k1<= m ; k1 ++) {  
     first=1;
 #ifdef windows  
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
 #endif    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
 #ifdef unix    /*    j1++;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);  */
 #endif    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 for (i=1; i<= nlstate ; i ++) {          scanf("%d", i);*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for (i=-5; i<=nlstate+ndeath; i++)  
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for (jk=-5; jk<=nlstate+ndeath; jk++)  
 }            for(m=iagemin; m <= iagemax+3; m++)
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              freq[i][jk][m]=0;
     for (i=1; i<= nlstate ; i ++) {        
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for (i=1; i<=nlstate; i++)  
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(m=iagemin; m <= iagemax+3; m++)
 }            prop[i][m]=0;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        
      for (i=1; i<= nlstate ; i ++) {        dateintsum=0;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        k2cpt=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for (i=1; i<=imx; i++) {
 }            bool=1;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
 #ifdef unix            for (z1=1; z1<=cptcoveff; z1++)       
 fprintf(ficgp,"\nset ter gif small size 400,300");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
 #endif                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                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", 
   }                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
   /*2 eme*/                  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*/
   for (k1=1; k1<= m ; k1 ++) {              } 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          }
       
     for (i=1; i<= nlstate+1 ; i ++) {          if (bool==1){
       k=2*i;            for(m=firstpass; m<=lastpass; m++){
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);              k2=anint[m][i]+(mint[m][i]/12.);
       for (j=1; j<= nlstate+1 ; j ++) {              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");                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 (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");                if (m<lastpass) {
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       for (j=1; j<= nlstate+1 ; j ++) {                }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                
         else fprintf(ficgp," \%%*lf (\%%*lf)");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
 }                    dateintsum=dateintsum+k2;
       fprintf(ficgp,"\" t\"\" w l 0,");                  k2cpt++;
      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 ++) {                /*}*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }          } /* end i */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");         
       else fprintf(ficgp,"\" t\"\" w l 0,");        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     }        pstamp(ficresp);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        if  (cptcovn>0) {
   }          fprintf(ficresp, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /*3eme*/          fprintf(ficresp, "**********\n#");
           fprintf(ficlog, "\n#********** Variable "); 
   for (k1=1; k1<= m ; k1 ++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for (cpt=1; cpt<= nlstate ; cpt ++) {          fprintf(ficlog, "**********\n#");
       k=2+nlstate*(cpt-1);        }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);        for(i=1; i<=nlstate;i++) 
       for (i=1; i< nlstate ; i ++) {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);        fprintf(ficresp, "\n");
       }        
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        for(i=iagemin; i <= iagemax+3; i++){
     }          if(i==iagemax+3){
   }            fprintf(ficlog,"Total");
            }else{
   /* CV preval stat */            if(first==1){
   for (k1=1; k1<= m ; k1 ++) {              first=0;
     for (cpt=1; cpt<nlstate ; cpt ++) {              printf("See log file for details...\n");
       k=3;            }
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);            fprintf(ficlog,"Age %d", i);
       for (i=1; i< nlstate ; i ++)          }
         fprintf(ficgp,"+$%d",k+i+1);          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                    pp[jk] += freq[jk][m][i]; 
       l=3+(nlstate+ndeath)*cpt;          }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          for(jk=1; jk <=nlstate ; jk++){
       for (i=1; i< nlstate ; i ++) {            for(m=-1, pos=0; m <=0 ; m++)
         l=3+(nlstate+ndeath)*cpt;              pos += freq[jk][m][i];
         fprintf(ficgp,"+$%d",l+i+1);            if(pp[jk]>=1.e-10){
       }              if(first==1){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                  printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              }
     }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }              }else{
               if(first==1)
   /* proba elementaires */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
    for(i=1,jk=1; i <=nlstate; i++){              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     for(k=1; k <=(nlstate+ndeath); k++){            }
       if (k != i) {          }
         for(j=1; j <=ncovmodel; j++){  
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/          for(jk=1; jk <=nlstate ; jk++){
           /*fprintf(ficgp,"%s",alph[1]);*/            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);              pp[jk] += freq[jk][m][i];
           jk++;          }       
           fprintf(ficgp,"\n");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         }            pos += pp[jk];
       }            posprop += prop[jk][i];
     }          }
     }          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
   for(jk=1; jk <=m; jk++) {              if(first==1)
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
    i=1;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
    for(k2=1; k2<=nlstate; k2++) {            }else{
      k3=i;              if(first==1)
      for(k=1; k<=(nlstate+ndeath); k++) {                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
        if (k != k2){              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            }
 ij=1;            if( i <= iagemax){
         for(j=3; j <=ncovmodel; j++) {              if(pos>=1.e-5){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                /*probs[i][jk][j1]= pp[jk]/pos;*/
             ij++;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
           }              }
           else              else
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
         }            }
           fprintf(ficgp,")/(1");          }
                  
         for(k1=1; k1 <=nlstate; k1++){            for(jk=-1; jk <=nlstate+ndeath; jk++)
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            for(m=-1; m <=nlstate+ndeath; m++)
 ij=1;              if(freq[jk][m][i] !=0 ) {
           for(j=3; j <=ncovmodel; j++){              if(first==1)
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
             ij++;              }
           }          if(i <= iagemax)
           else            fprintf(ficresp,"\n");
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          if(first==1)
           }            printf("Others in log...\n");
           fprintf(ficgp,")");          fprintf(ficlog,"\n");
         }        }
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        /*}*/
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    }
         i=i+ncovmodel;    dateintmean=dateintsum/k2cpt; 
        }   
      }    fclose(ficresp);
    }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    free_vector(pp,1,nlstate);
   }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
        /* End of Freq */
   fclose(ficgp);  }
   /* end gnuplot */  
      /************ Prevalence ********************/
 chdir(path);  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
      {  
     free_ivector(wav,1,imx);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);       in each health status at the date of interview (if between dateprev1 and dateprev2).
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);         We still use firstpass and lastpass as another selection.
     free_ivector(num,1,n);    */
     free_vector(agedc,1,n);   
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    int i, m, jk, j1, bool, z1,j;
     fclose(ficparo);  
     fclose(ficres);    double **prop;
     /*  }*/    double posprop; 
        double  y2; /* in fractional years */
    /*________fin mle=1_________*/    int iagemin, iagemax;
        int first; /** to stop verbosity which is redirected to log file */
   
      iagemin= (int) agemin;
     /* No more information from the sample is required now */    iagemax= (int) agemax;
   /* Reads comments: lines beginning with '#' */    /*pp=vector(1,nlstate);*/
   while((c=getc(ficpar))=='#' && c!= EOF){    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     ungetc(c,ficpar);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     fgets(line, MAXLINE, ficpar);    j1=0;
     puts(line);    
     fputs(line,ficparo);    /*j=cptcoveff;*/
   }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   ungetc(c,ficpar);    
      first=1;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);      /*for(i1=1; i1<=ncodemax[k1];i1++){
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        j1++;*/
 /*--------- index.htm --------*/        
         for (i=1; i<=nlstate; i++)  
   strcpy(optionfilehtm,optionfile);          for(m=iagemin; m <= iagemax+3; m++)
   strcat(optionfilehtm,".htm");            prop[i][m]=0.0;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {       
     printf("Problem with %s \n",optionfilehtm);goto end;        for (i=1; i<=imx; i++) { /* Each individual */
   }          bool=1;
           if  (cptcovn>0) {
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">            for (z1=1; z1<=cptcoveff; z1++) 
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 Total number of observations=%d <br>                bool=0;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>          } 
 <hr  size=\"2\" color=\"#EC5E5E\">          if (bool==1) { 
 <li>Outputs files<br><br>\n            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>                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); 
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>                if (s[m][i]>0 && s[m][i]<=nlstate) { 
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>                  /*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]]);*/
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>                  prop[s[m][i]][iagemax+3] += weight[i]; 
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>                } 
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);              }
             } /* end selection of waves */
  fprintf(fichtm," <li>Graphs</li><p>");          }
         }
  m=cptcoveff;        for(i=iagemin; i <= iagemax+3; i++){  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
  j1=0;          } 
  for(k1=1; k1<=m;k1++){          
    for(i1=1; i1<=ncodemax[k1];i1++){          for(jk=1; jk <=nlstate ; jk++){     
        j1++;            if( i <=  iagemax){ 
        if (cptcovn > 0) {              if(posprop>=1.e-5){ 
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");                probs[i][jk][j1]= prop[jk][i]/posprop;
          for (cpt=1; cpt<=cptcoveff;cpt++)              } else{
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);                if(first==1){
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");                  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]);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>                }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);                  }
        for(cpt=1; cpt<nlstate;cpt++){            } 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          }/* end jk */ 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        }/* end i */ 
        }      /*} *//* end i1 */
     for(cpt=1; cpt<=nlstate;cpt++) {    } /* end j1 */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    
 interval) in state (%d): v%s%d%d.gif <br>    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      /*free_vector(pp,1,nlstate);*/
      }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
      for(cpt=1; cpt<=nlstate;cpt++) {  }  /* End of prevalence */
         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,j1,strtok(optionfile, "."),cpt,j1);  /************* Waves Concatenation ***************/
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  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)
 health expectancies in states (1) and (2): e%s%d.gif<br>  {
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 fprintf(fichtm,"\n</body>");       Death is a valid wave (if date is known).
    }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
  }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
 fclose(fichtm);       and mw[mi+1][i]. dh depends on stepm.
        */
   /*--------------- Prevalence limit --------------*/  
      int i, mi, m;
   strcpy(filerespl,"pl");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   strcat(filerespl,fileres);       double sum=0., jmean=0.;*/
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    int first;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    int j, k=0,jk, ju, jl;
   }    double sum=0.;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    first=0;
   fprintf(ficrespl,"#Prevalence limit\n");    jmin=100000;
   fprintf(ficrespl,"#Age ");    jmax=-1;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    jmean=0.;
   fprintf(ficrespl,"\n");    for(i=1; i<=imx; i++){
        mi=0;
   prlim=matrix(1,nlstate,1,nlstate);      m=firstpass;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      while(s[m][i] <= nlstate){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          mw[++mi][i]=m;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if(m >=lastpass)
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          break;
   k=0;        else
   agebase=agemin;          m++;
   agelim=agemax;      }/* end while */
   ftolpl=1.e-10;      if (s[m][i] > nlstate){
   i1=cptcoveff;        mi++;     /* Death is another wave */
   if (cptcovn < 1){i1=1;}        /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
   for(cptcov=1;cptcov<=i1;cptcov++){        mw[mi][i]=m;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      wav[i]=mi;
         fprintf(ficrespl,"\n#******");      if(mi==0){
         for(j=1;j<=cptcoveff;j++)        nbwarn++;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if(first==0){
         fprintf(ficrespl,"******\n");          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
                  first=1;
         for (age=agebase; age<=agelim; age++){        }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        if(first==1){
           fprintf(ficrespl,"%.0f",age );          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
           for(i=1; i<=nlstate;i++)        }
           fprintf(ficrespl," %.5f", prlim[i][i]);      } /* end mi==0 */
           fprintf(ficrespl,"\n");    } /* End individuals */
         }  
       }    for(i=1; i<=imx; i++){
     }      for(mi=1; mi<wav[i];mi++){
   fclose(ficrespl);        if (stepm <=0)
           dh[mi][i]=1;
   /*------------- h Pij x at various ages ------------*/        else{
            if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);            if (agedc[i] < 2*AGESUP) {
   if((ficrespij=fopen(filerespij,"w"))==NULL) {              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;              if(j==0) j=1;  /* Survives at least one month after exam */
   }              else if(j<0){
   printf("Computing pij: result on file '%s' \n", filerespij);                nberr++;
                  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]);
   stepsize=(int) (stepm+YEARM-1)/YEARM;                j=1; /* Temporary Dangerous patch */
   /*if (stepm<=24) stepsize=2;*/                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                 fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   agelim=AGESUP;                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);
   hstepm=stepsize*YEARM; /* Every year of age */              }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */              k=k+1;
                if (j >= jmax){
   k=0;                jmax=j;
   for(cptcov=1;cptcov<=i1;cptcov++){                ijmax=i;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              }
       k=k+1;              if (j <= jmin){
         fprintf(ficrespij,"\n#****** ");                jmin=j;
         for(j=1;j<=cptcoveff;j++)                ijmin=i;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              }
         fprintf(ficrespij,"******\n");              sum=sum+j;
                      /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            }
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          else{
           oldm=oldms;savm=savms;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
           fprintf(ficrespij,"# Age");  
           for(i=1; i<=nlstate;i++)            k=k+1;
             for(j=1; j<=nlstate+ndeath;j++)            if (j >= jmax) {
               fprintf(ficrespij," %1d-%1d",i,j);              jmax=j;
           fprintf(ficrespij,"\n");              ijmax=i;
           for (h=0; h<=nhstepm; h++){            }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );            else if (j <= jmin){
             for(i=1; i<=nlstate;i++)              jmin=j;
               for(j=1; j<=nlstate+ndeath;j++)              ijmin=i;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            }
             fprintf(ficrespij,"\n");            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           }            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if(j<0){
           fprintf(ficrespij,"\n");              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]);
     }              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   }            }
             sum=sum+j;
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/          }
           jk= j/stepm;
   fclose(ficrespij);          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
   if(stepm == 1) {          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   /*---------- Forecasting ------------------*/            if(jl==0){
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;              dh[mi][i]=jk;
               bh[mi][i]=0;
   /*printf("calage= %f", calagedate);*/            }else{ /* We want a negative bias in order to only have interpolation ie
                      * to avoid the price of an extra matrix product in likelihood */
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
             }
   strcpy(fileresf,"f");          }else{
   strcat(fileresf,fileres);            if(jl <= -ju){
   if((ficresf=fopen(fileresf,"w"))==NULL) {              dh[mi][i]=jk;
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;              bh[mi][i]=jl;       /* bias is positive if real duration
   }                                   * is higher than the multiple of stepm and negative otherwise.
   printf("Computing forecasting: result on file '%s' \n", fileresf);                                   */
             }
   free_matrix(mint,1,maxwav,1,n);            else{
   free_matrix(anint,1,maxwav,1,n);              dh[mi][i]=jk+1;
   free_matrix(agev,1,maxwav,1,imx);              bh[mi][i]=ju;
   /* Mobile average */            }
             if(dh[mi][i]==0){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
   if (mobilav==1) {              /*  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);*/
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)          } /* end if mle */
       for (i=1; i<=nlstate;i++)        }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      } /* end wave */
           mobaverage[(int)agedeb][i][cptcod]=0.;    }
        jmean=sum/k;
     for (agedeb=bage+4; agedeb<=fage; agedeb++){    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);
       for (i=1; i<=nlstate;i++){    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);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){   }
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  /*********** Tricode ****************************/
           }  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  {
         }    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
       }    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
     }      /* Boring subroutine which should only output nbcode[Tvar[j]][k]
   }     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
     /* nbcode[Tvar[j]][1]= 
   stepsize=(int) (stepm+YEARM-1)/YEARM;    */
   if (stepm<=12) stepsize=1;  
     int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   agelim=AGESUP;    int modmaxcovj=0; /* Modality max of covariates j */
   /*hstepm=stepsize*YEARM; *//* Every year of age */    int cptcode=0; /* Modality max of covariates j */
   hstepm=1;    int modmincovj=0; /* Modality min of covariates j */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */  
   yp1=modf(dateintmean,&yp);  
   anprojmean=yp;    cptcoveff=0; 
   yp2=modf((yp1*12),&yp);   
   mprojmean=yp;    for (k=-1; k < maxncov; k++) Ndum[k]=0;
   yp1=modf((yp2*30.5),&yp);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;    /* Loop on covariates without age and products */
   if(mprojmean==0) jprojmean=1;    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
       for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);                                 modality of this covariate Vj*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
   if (popforecast==1) {                                      * If product of Vn*Vm, still boolean *:
     if((ficpop=fopen(popfile,"r"))==NULL)    {                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
       printf("Problem with population file : %s\n",popfile);goto end;                                      * 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
     popage=ivector(0,AGESUP);                                        modality of the nth covariate of individual i. */
     popeffectif=vector(0,AGESUP);        if (ij > modmaxcovj)
     popcount=vector(0,AGESUP);          modmaxcovj=ij; 
         else if (ij < modmincovj) 
     i=1;            modmincovj=ij; 
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)        if ((ij < -1) && (ij > NCOVMAX)){
       {          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
         i=i+1;          exit(1);
       }        }else
     imx=i;        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
            /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   }        /* getting the maximum value of the modality of the covariate
            (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
   for(cptcov=1;cptcov<=i1;cptcov++){           female is 1, then modmaxcovj=1.*/
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      }
       k=k+1;      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       fprintf(ficresf,"\n#******");      cptcode=modmaxcovj;
       for(j=1;j<=cptcoveff;j++) {      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     /*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 */
       fprintf(ficresf,"******\n");        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
       fprintf(ficresf,"# StartingAge FinalAge");        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
       if (popforecast==1)  fprintf(ficresf," [Population]");        }
            /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
       for (cpt=0; cpt<4;cpt++) {           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
         fprintf(ficresf,"\n");      } /* Ndum[-1] number of undefined modalities */
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
       /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
         nhstepm = nhstepm/hstepm;         modmincovj=3; modmaxcovj = 7;
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
          which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         variables V1_1 and V1_2.
         oldm=oldms;savm=savms;         nbcode[Tvar[j]][ij]=k;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);           nbcode[Tvar[j]][1]=0;
                 nbcode[Tvar[j]][2]=1;
         for (h=0; h<=nhstepm; h++){         nbcode[Tvar[j]][3]=2;
           if (h==(int) (calagedate+YEARM*cpt)) {      */
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);      ij=1; /* ij is similar to i but can jumps over null modalities */
           }      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
           for(j=1; j<=nlstate+ndeath;j++) {        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
             kk1=0.;kk2=0;          /*recode from 0 */
             for(i=1; i<=nlstate;i++) {                  if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
               if (mobilav==1)            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                                       k is a modality. If we have model=V1+V1*sex 
               else {                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            ij++;
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/          }
               }          if (ij > ncodemax[j]) break; 
         }  /* end of loop on */
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];      } /* 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*/  
              
             if (h==(int)(calagedate+12*cpt)){   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
               fprintf(ficresf," %.3f", kk1);    
                  for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
             }     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
           }     Ndum[ij]++; 
         }   } 
         /*      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);*/  
       }   ij=1;
       }   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
     }     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   }     if((Ndum[i]!=0) && (i<=ncovcol)){
   /*  if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
   if (popforecast==1) {       Tvaraff[ij]=i; /*For printing (unclear) */
     free_ivector(popage,0,AGESUP);       ij++;
     free_vector(popeffectif,0,AGESUP);     }else
     free_vector(popcount,0,AGESUP);         Tvaraff[ij]=0;
   }   }
   free_imatrix(s,1,maxwav+1,1,n);   ij--;
   free_vector(weight,1,n);*/   cptcoveff=ij; /*Number of total covariates*/
   fclose(ficresf);  
   }/* End forecasting */  }
   else{  
     erreur=108;  
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);  /*********** Health Expectancies ****************/
   }  
   void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   /*---------- Health expectancies and variances ------------*/  
   {
   strcpy(filerest,"t");    /* Health expectancies, no variances */
   strcat(filerest,fileres);    int i, j, nhstepm, hstepm, h, nstepm;
   if((ficrest=fopen(filerest,"w"))==NULL) {    int nhstepma, nstepma; /* Decreasing with age */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    double age, agelim, hf;
   }    double ***p3mat;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    double eip;
   
     pstamp(ficreseij);
   strcpy(filerese,"e");    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   strcat(filerese,fileres);    fprintf(ficreseij,"# Age");
   if((ficreseij=fopen(filerese,"w"))==NULL) {    for(i=1; i<=nlstate;i++){
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      for(j=1; j<=nlstate;j++){
   }        fprintf(ficreseij," e%1d%1d ",i,j);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      }
       fprintf(ficreseij," e%1d. ",i);
  strcpy(fileresv,"v");    }
   strcat(fileresv,fileres);    fprintf(ficreseij,"\n");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    
   }    if(estepm < stepm){
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   k=0;    else  hstepm=estepm;   
   for(cptcov=1;cptcov<=i1;cptcov++){    /* We compute the life expectancy from trapezoids spaced every estepm months
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     * This is mainly to measure the difference between two models: for example
       k=k+1;     * if stepm=24 months pijx are given only every 2 years and by summing them
       fprintf(ficrest,"\n#****** ");     * we are calculating an estimate of the Life Expectancy assuming a linear 
       for(j=1;j<=cptcoveff;j++)     * progression in between and thus overestimating or underestimating according
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     * to the curvature of the survival function. If, for the same date, we 
       fprintf(ficrest,"******\n");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
       fprintf(ficreseij,"\n#****** ");     * hypothesis. A more precise result, taking into account a more precise
       for(j=1;j<=cptcoveff;j++)     * curvature will be obtained if estepm is as small as stepm. */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");    /* 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. 
       fprintf(ficresvij,"\n#****** ");       nhstepm is the number of hstepm from age to agelim 
       for(j=1;j<=cptcoveff;j++)       nstepm is the number of stepm from age to agelin. 
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);       Look at hpijx to understand the reason of that which relies in memory size
       fprintf(ficresvij,"******\n");       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       survival function given by stepm (the optimization length). Unfortunately it
       oldm=oldms;savm=savms;       means that if the survival funtion is printed only each two years of age and if
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);         you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       results. So we changed our mind and took the option of the best precision.
       oldm=oldms;savm=savms;    */
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
        
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    agelim=AGESUP;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    /* If stepm=6 months */
       fprintf(ficrest,"\n");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
                 in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       hf=1;      
       if (stepm >= YEARM) hf=stepm/YEARM;  /* nhstepm age range expressed in number of stepm */
       epj=vector(1,nlstate+1);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       for(age=bage; age <=fage ;age++){    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    /* if (stepm >= YEARM) hstepm=1;*/
         if (popbased==1) {    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           for(i=1; i<=nlstate;i++)    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             prlim[i][i]=probs[(int)age][i][k];  
         }    for (age=bage; age<=fage; age ++){ 
              nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         fprintf(ficrest," %.0f",age);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      /* if (stepm >= YEARM) hstepm=1;*/
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  
           }      /* If stepm=6 months */
           epj[nlstate+1] +=epj[j];      /* Computed by stepm unit matrices, product of hstepma matrices, stored
         }         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
         for(i=1, vepp=0.;i <=nlstate;i++)      
           for(j=1;j <=nlstate;j++)      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
             vepp += vareij[i][j][(int)age];      
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         for(j=1;j <=nlstate;j++){      
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));      printf("%d|",(int)age);fflush(stdout);
         }      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         fprintf(ficrest,"\n");      
       }      /* Computing expectancies */
     }      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++)
                  for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                    eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
             /* 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]);*/
  fclose(ficreseij);  
  fclose(ficresvij);          }
   fclose(ficrest);  
   fclose(ficpar);      fprintf(ficreseij,"%3.0f",age );
   free_vector(epj,1,nlstate+1);      for(i=1; i<=nlstate;i++){
   /*  scanf("%d ",i); */        eip=0;
         for(j=1; j<=nlstate;j++){
   /*------- Variance limit prevalence------*/            eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
 strcpy(fileresvpl,"vpl");        }
   strcat(fileresvpl,fileres);        fprintf(ficreseij,"%9.4f", eip );
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      fprintf(ficreseij,"\n");
     exit(0);      
   }    }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
  k=0;    fprintf(ficlog,"\n");
  for(cptcov=1;cptcov<=i1;cptcov++){    
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  }
      k=k+1;  
      fprintf(ficresvpl,"\n#****** ");  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
      for(j=1;j<=cptcoveff;j++)  
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  {
      fprintf(ficresvpl,"******\n");    /* Covariances of health expectancies eij and of total life expectancies according
           to initial status i, ei. .
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    */
      oldm=oldms;savm=savms;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    int nhstepma, nstepma; /* Decreasing with age */
    }    double age, agelim, hf;
  }    double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
   fclose(ficresvpl);    double *xp, *xm;
     double **gp, **gm;
   /*---------- End : free ----------------*/    double ***gradg, ***trgradg;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    int theta;
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double eip, vip;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
      varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
      xp=vector(1,npar);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    xm=vector(1,npar);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    
      pstamp(ficresstdeij);
   free_matrix(matcov,1,npar,1,npar);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   free_vector(delti,1,npar);    fprintf(ficresstdeij,"# Age");
      for(i=1; i<=nlstate;i++){
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   if(erreur >0)      fprintf(ficresstdeij," e%1d. ",i);
     printf("End of Imach with error %d\n",erreur);    }
   else   printf("End of Imach\n");    fprintf(ficresstdeij,"\n");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
      pstamp(ficrescveij);
   /* 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);*/    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   /*printf("Total time was %d uSec.\n", total_usecs);*/    fprintf(ficrescveij,"# Age");
   /*------ End -----------*/    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
  end:        for(i2=1; i2<=nlstate;i2++)
 #ifdef windows          for(j2=1; j2<=nlstate;j2++){
   /* chdir(pathcd);*/            cptj2= (j2-1)*nlstate+i2;
 #endif            if(cptj2 <= cptj)
  /*system("wgnuplot graph.plt");*/              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
  /*system("../gp37mgw/wgnuplot graph.plt");*/          }
  /*system("cd ../gp37mgw");*/      }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    fprintf(ficrescveij,"\n");
  strcpy(plotcmd,GNUPLOTPROGRAM);    
  strcat(plotcmd," ");    if(estepm < stepm){
  strcat(plotcmd,optionfilegnuplot);      printf ("Problem %d lower than %d\n",estepm, stepm);
  system(plotcmd);    }
     else  hstepm=estepm;   
 #ifdef windows    /* We compute the life expectancy from trapezoids spaced every estepm months
   while (z[0] != 'q') {     * This is mainly to measure the difference between two models: for example
     chdir(path);     * if stepm=24 months pijx are given only every 2 years and by summing them
     printf("\nType e to edit output files, c to start again, and q for exiting: ");     * we are calculating an estimate of the Life Expectancy assuming a linear 
     scanf("%s",z);     * progression in between and thus overestimating or underestimating according
     if (z[0] == 'c') system("./imach");     * to the curvature of the survival function. If, for the same date, we 
     else if (z[0] == 'e') {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       chdir(path);     * to compare the new estimate of Life expectancy with the same linear 
       system(optionfilehtm);     * hypothesis. A more precise result, taking into account a more precise
     }     * curvature will be obtained if estepm is as small as stepm. */
     else if (z[0] == 'q') exit(0);  
   }    /* For example we decided to compute the life expectancy with the smallest unit */
 #endif    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 }       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
       /* 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 */
       
       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
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           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);  
     
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
           }
         }
        
         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];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       
   
        for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
   
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
             /* 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]);*/
   
           }
   
       fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     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);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     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);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     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(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at function hpijx to understand why (it is linked to memory size questions) */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  k1, l1, tj;
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, 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 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, cptcod, i, h, i1;
     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];
     int i,j, k, 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 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=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     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 */
       strcpy(line, linetmp);
     
   
       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  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=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *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=0, fage=110, 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 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";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.23  
changed lines
  Added in v.1.166


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