Diff for /imach/src/imach.c between versions 1.12 and 1.165

version 1.12, 2002/02/20 16:57:00 version 1.165, 2014/12/16 11:20:36
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.165  2014/12/16 11:20:36  brouard
   individuals from different ages are interviewed on their health status    Summary: After compiling on Visual C
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    * imach.c (Module): Merging 1.61 to 1.162
   Health expectancies are computed from the transistions observed between  
   waves and are computed for each degree of severity of disability (number    Revision 1.164  2014/12/16 10:52:11  brouard
   of life states). More degrees you consider, more time is necessary to    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
   reach the Maximum Likelihood of the parameters involved in the model.  
   The simplest model is the multinomial logistic model where pij is    * imach.c (Module): Merging 1.61 to 1.162
   the probabibility to be observed in state j at the second wave conditional  
   to be observed in state i at the first wave. Therefore the model is:    Revision 1.163  2014/12/16 10:30:11  brouard
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    * imach.c (Module): Merging 1.61 to 1.162
   is a covariate. If you want to have a more complex model than "constant and  
   age", you should modify the program where the markup    Revision 1.162  2014/09/25 11:43:39  brouard
     *Covariates have to be included here again* invites you to do it.    Summary: temporary backup 0.99!
   More covariates you add, less is the speed of the convergence.  
     Revision 1.1  2014/09/16 11:06:58  brouard
   The advantage that this computer programme claims, comes from that if the    Summary: With some code (wrong) for nlopt
   delay between waves is not identical for each individual, or if some  
   individual missed an interview, the information is not rounded or lost, but    Author:
   taken into account using an interpolation or extrapolation.  
   hPijx is the probability to be    Revision 1.161  2014/09/15 20:41:41  brouard
   observed in state i at age x+h conditional to the observed state i at age    Summary: Problem with macro SQR on Intel compiler
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    Revision 1.160  2014/09/02 09:24:05  brouard
   quarter trimester, semester or year) is model as a multinomial logistic.    *** empty log message ***
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply hPijx.    Revision 1.159  2014/09/01 10:34:10  brouard
     Summary: WIN32
   Also this programme outputs the covariance matrix of the parameters but also    Author: Brouard
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.158  2014/08/27 17:11:51  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    *** empty log message ***
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.157  2014/08/27 16:26:55  brouard
   from the European Union.    Summary: Preparing windows Visual studio version
   It is copyrighted identically to a GNU software product, ie programme and    Author: Brouard
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    In order to compile on Visual studio, time.h is now correct and time_t
   **********************************************************************/    and tm struct should be used. difftime should be used but sometimes I
      just make the differences in raw time format (time(&now).
 #include <math.h>    Trying to suppress #ifdef LINUX
 #include <stdio.h>    Add xdg-open for __linux in order to open default browser.
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.156  2014/08/25 20:10:10  brouard
     *** empty log message ***
 #define MAXLINE 256  
 #define FILENAMELENGTH 80    Revision 1.155  2014/08/25 18:32:34  brouard
 /*#define DEBUG*/    Summary: New compile, minor changes
 #define windows    Author: Brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.154  2014/06/20 17:32:08  brouard
     Summary: Outputs now all graphs of convergence to period prevalence
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.153  2014/06/20 16:45:46  brouard
     Summary: If 3 live state, convergence to period prevalence on same graph
 #define NINTERVMAX 8    Author: Brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.152  2014/06/18 17:54:09  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.151  2014/06/18 16:43:30  brouard
 #define AGESUP 130    *** empty log message ***
 #define AGEBASE 40  
     Revision 1.150  2014/06/18 16:42:35  brouard
     Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 int nvar;    Author: brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.149  2014/06/18 15:51:14  brouard
 int nlstate=2; /* Number of live states */    Summary: Some fixes in parameter files errors
 int ndeath=1; /* Number of dead states */    Author: Nicolas Brouard
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
     Revision 1.148  2014/06/17 17:38:48  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    Summary: Nothing new
 int maxwav; /* Maxim number of waves */    Author: Brouard
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Just a new packaging for OS/X version 0.98nS
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.147  2014/06/16 10:33:11  brouard
 double jmean; /* Mean space between 2 waves */    *** empty log message ***
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.146  2014/06/16 10:20:28  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    Summary: Merge
 FILE *ficgp, *fichtm;    Author: Brouard
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Merge, before building revised version.
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.145  2014/06/10 21:23:15  brouard
  FILE  *ficresvpl;    Summary: Debugging with valgrind
   char fileresvpl[FILENAMELENGTH];    Author: Nicolas Brouard
   
 #define NR_END 1    Lot of changes in order to output the results with some covariates
 #define FREE_ARG char*    After the Edimburgh REVES conference 2014, it seems mandatory to
 #define FTOL 1.0e-10    improve the code.
     No more memory valgrind error but a lot has to be done in order to
 #define NRANSI    continue the work of splitting the code into subroutines.
 #define ITMAX 200    Also, decodemodel has been improved. Tricode is still not
     optimal. nbcode should be improved. Documentation has been added in
 #define TOL 2.0e-4    the source code.
   
 #define CGOLD 0.3819660    Revision 1.143  2014/01/26 09:45:38  brouard
 #define ZEPS 1.0e-10    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define GOLD 1.618034    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    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
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.141  2014/01/26 02:42:01  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define rint(a) floor(a+0.5)  
     Revision 1.140  2011/09/02 10:37:54  brouard
 static double sqrarg;    Summary: times.h is ok with mingw32 now.
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.139  2010/06/14 07:50:17  brouard
     After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 int imx;    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.138  2010/04/30 18:19:40  brouard
     *** empty log message ***
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.137  2010/04/29 18:11:38  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (Module): Checking covariates for more complex models
 double **pmmij;    than V1+V2. A lot of change to be done. Unstable.
   
 double *weight;    Revision 1.136  2010/04/26 20:30:53  brouard
 int **s; /* Status */    (Module): merging some libgsl code. Fixing computation
 double *agedc, **covar, idx;    of likelione (using inter/intrapolation if mle = 0) in order to
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    get same likelihood as if mle=1.
     Some cleaning of code and comments added.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.135  2009/10/29 15:33:14  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name )    Revision 1.134  2009/10/29 13:18:53  brouard
 {    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.133  2009/07/06 10:21:25  brouard
     just nforces
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.132  2009/07/06 08:22:05  brouard
    s = strrchr( path, '\\' );           /* find last / */    Many tings
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.131  2009/06/20 16:22:47  brouard
       extern char       *getwd( );    Some dimensions resccaled
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.130  2009/05/26 06:44:34  brouard
 #else    (Module): Max Covariate is now set to 20 instead of 8. A
       extern char       *getcwd( );    lot of cleaning with variables initialized to 0. Trying to make
     V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.129  2007/08/31 13:49:27  lievre
          return( GLOCK_ERROR_GETCWD );    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.128  2006/06/30 13:02:05  brouard
    } else {                             /* strip direcotry from path */    (Module): Clarifications on computing e.j
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Revision 1.127  2006/04/28 18:11:50  brouard
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): Yes the sum of survivors was wrong since
       strcpy( name, s );                /* save file name */    imach-114 because nhstepm was no more computed in the age
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    loop. Now we define nhstepma in the age loop.
       dirc[l1-l2] = 0;                  /* add zero */    (Module): In order to speed up (in case of numerous covariates) we
    }    compute health expectancies (without variances) in a first step
    l1 = strlen( dirc );                 /* length of directory */    and then all the health expectancies with variances or standard
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    deviation (needs data from the Hessian matrices) which slows the
    return( 0 );                         /* we're done */    computation.
 }    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
   
 /******************************************/    Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
 void replace(char *s, char*t)    imach-114 because nhstepm was no more computed in the age
 {    loop. Now we define nhstepma in the age loop.
   int i;    Version 0.98h
   int lg=20;  
   i=0;    Revision 1.125  2006/04/04 15:20:31  lievre
   lg=strlen(t);    Errors in calculation of health expectancies. Age was not initialized.
   for(i=0; i<= lg; i++) {    Forecasting file added.
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.124  2006/03/22 17:13:53  lievre
   }    Parameters are printed with %lf instead of %f (more numbers after the comma).
 }    The log-likelihood is printed in the log file
   
 int nbocc(char *s, char occ)    Revision 1.123  2006/03/20 10:52:43  brouard
 {    * imach.c (Module): <title> changed, corresponds to .htm file
   int i,j=0;    name. <head> headers where missing.
   int lg=20;  
   i=0;    * imach.c (Module): Weights can have a decimal point as for
   lg=strlen(s);    English (a comma might work with a correct LC_NUMERIC environment,
   for(i=0; i<= lg; i++) {    otherwise the weight is truncated).
   if  (s[i] == occ ) j++;    Modification of warning when the covariates values are not 0 or
   }    1.
   return j;    Version 0.98g
 }  
     Revision 1.122  2006/03/20 09:45:41  brouard
 void cutv(char *u,char *v, char*t, char occ)    (Module): Weights can have a decimal point as for
 {    English (a comma might work with a correct LC_NUMERIC environment,
   int i,lg,j,p=0;    otherwise the weight is truncated).
   i=0;    Modification of warning when the covariates values are not 0 or
   for(j=0; j<=strlen(t)-1; j++) {    1.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Version 0.98g
   }  
     Revision 1.121  2006/03/16 17:45:01  lievre
   lg=strlen(t);    * imach.c (Module): Comments concerning covariates added
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    * imach.c (Module): refinements in the computation of lli if
   }    status=-2 in order to have more reliable computation if stepm is
      u[p]='\0';    not 1 month. Version 0.98f
   
    for(j=0; j<= lg; j++) {    Revision 1.120  2006/03/16 15:10:38  lievre
     if (j>=(p+1))(v[j-p-1] = t[j]);    (Module): refinements in the computation of lli if
   }    status=-2 in order to have more reliable computation if stepm is
 }    not 1 month. Version 0.98f
   
 /********************** nrerror ********************/    Revision 1.119  2006/03/15 17:42:26  brouard
     (Module): Bug if status = -2, the loglikelihood was
 void nrerror(char error_text[])    computed as likelihood omitting the logarithm. Version O.98e
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.118  2006/03/14 18:20:07  brouard
   fprintf(stderr,"%s\n",error_text);    (Module): varevsij Comments added explaining the second
   exit(1);    table of variances if popbased=1 .
 }    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 /*********************** vector *******************/    (Module): Function pstamp added
 double *vector(int nl, int nh)    (Module): Version 0.98d
 {  
   double *v;    Revision 1.117  2006/03/14 17:16:22  brouard
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    (Module): varevsij Comments added explaining the second
   if (!v) nrerror("allocation failure in vector");    table of variances if popbased=1 .
   return v-nl+NR_END;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 }    (Module): Function pstamp added
     (Module): Version 0.98d
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.116  2006/03/06 10:29:27  brouard
 {    (Module): Variance-covariance wrong links and
   free((FREE_ARG)(v+nl-NR_END));    varian-covariance of ej. is needed (Saito).
 }  
     Revision 1.115  2006/02/27 12:17:45  brouard
 /************************ivector *******************************/    (Module): One freematrix added in mlikeli! 0.98c
 int *ivector(long nl,long nh)  
 {    Revision 1.114  2006/02/26 12:57:58  brouard
   int *v;    (Module): Some improvements in processing parameter
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    filename with strsep.
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;    Revision 1.113  2006/02/24 14:20:24  brouard
 }    (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
 /******************free ivector **************************/    allocation too.
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.112  2006/01/30 09:55:26  brouard
   free((FREE_ARG)(v+nl-NR_END));    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 }  
     Revision 1.111  2006/01/25 20:38:18  brouard
 /******************* imatrix *******************************/    (Module): Lots of cleaning and bugs added (Gompertz)
 int **imatrix(long nrl, long nrh, long ncl, long nch)    (Module): Comments can be added in data file. Missing date values
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    can be a simple dot '.'.
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Revision 1.110  2006/01/25 00:51:50  brouard
   int **m;    (Module): Lots of cleaning and bugs added (Gompertz)
    
   /* allocate pointers to rows */    Revision 1.109  2006/01/24 19:37:15  brouard
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    (Module): Comments (lines starting with a #) are allowed in data.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.108  2006/01/19 18:05:42  lievre
   m -= nrl;    Gnuplot problem appeared...
      To be fixed
    
   /* allocate rows and set pointers to them */    Revision 1.107  2006/01/19 16:20:37  brouard
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Test existence of gnuplot in imach path
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.106  2006/01/19 13:24:36  brouard
   m[nrl] -= ncl;    Some cleaning and links added in html output
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    Revision 1.105  2006/01/05 20:23:19  lievre
      *** empty log message ***
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.104  2005/09/30 16:11:43  lievre
 }    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
 /****************** free_imatrix *************************/    that the person is alive, then we can code his/her status as -2
 void free_imatrix(m,nrl,nrh,ncl,nch)    (instead of missing=-1 in earlier versions) and his/her
       int **m;    contributions to the likelihood is 1 - Prob of dying from last
       long nch,ncl,nrh,nrl;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
      /* free an int matrix allocated by imatrix() */    the healthy state at last known wave). Version is 0.98
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    Revision 1.103  2005/09/30 15:54:49  lievre
   free((FREE_ARG) (m+nrl-NR_END));    (Module): sump fixed, loop imx fixed, and simplifications.
 }  
     Revision 1.102  2004/09/15 17:31:30  brouard
 /******************* matrix *******************************/    Add the possibility to read data file including tab characters.
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {    Revision 1.101  2004/09/15 10:38:38  brouard
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    Fix on curr_time
   double **m;  
     Revision 1.100  2004/07/12 18:29:06  brouard
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Add version for Mac OS X. Just define UNIX in Makefile
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.99  2004/06/05 08:57:40  brouard
   m -= nrl;    *** empty log message ***
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Revision 1.98  2004/05/16 15:05:56  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    New version 0.97 . First attempt to estimate force of mortality
   m[nrl] += NR_END;    directly from the data i.e. without the need of knowing the health
   m[nrl] -= ncl;    state at each age, but using a Gompertz model: log u =a + b*age .
     This is the basic analysis of mortality and should be done before any
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    other analysis, in order to test if the mortality estimated from the
   return m;    cross-longitudinal survey is different from the mortality estimated
 }    from other sources like vital statistic data.
   
 /*************************free matrix ************************/    The same imach parameter file can be used but the option for mle should be -3.
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {    Agnès, who wrote this part of the code, tried to keep most of the
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    former routines in order to include the new code within the former code.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    The output is very simple: only an estimate of the intercept and of
     the slope with 95% confident intervals.
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Current limitations:
 {    A) Even if you enter covariates, i.e. with the
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   double ***m;    B) There is no computation of Life Expectancy nor Life Table.
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.97  2004/02/20 13:25:42  lievre
   if (!m) nrerror("allocation failure 1 in matrix()");    Version 0.96d. Population forecasting command line is (temporarily)
   m += NR_END;    suppressed.
   m -= nrl;  
     Revision 1.96  2003/07/15 15:38:55  brouard
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    rewritten within the same printf. Workaround: many printfs.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
   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 1.94  2003/06/27 13:00:02  brouard
   m[nrl][ncl] += NR_END;    Just cleaning
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)    Revision 1.93  2003/06/25 16:33:55  brouard
     m[nrl][j]=m[nrl][j-1]+nlay;    (Module): On windows (cygwin) function asctime_r doesn't
      exist so I changed back to asctime which exists.
   for (i=nrl+1; i<=nrh; i++) {    (Module): Version 0.96b
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    Revision 1.92  2003/06/25 16:30:45  brouard
       m[i][j]=m[i][j-1]+nlay;    (Module): On windows (cygwin) function asctime_r doesn't
   }    exist so I changed back to asctime which exists.
   return m;  
 }    Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
 /*************************free ma3x ************************/    (Repository): Elapsed time after each iteration is now output. It
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    helps to forecast when convergence will be reached. Elapsed time
 {    is stamped in powell.  We created a new html file for the graphs
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    concerning matrix of covariance. It has extension -cov.htm.
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    Revision 1.90  2003/06/24 12:34:15  brouard
 }    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 /***************** f1dim *************************/    of the covariance matrix to be input.
 extern int ncom;  
 extern double *pcom,*xicom;    Revision 1.89  2003/06/24 12:30:52  brouard
 extern double (*nrfunc)(double []);    (Module): Some bugs corrected for windows. Also, when
      mle=-1 a template is output in file "or"mypar.txt with the design
 double f1dim(double x)    of the covariance matrix to be input.
 {  
   int j;    Revision 1.88  2003/06/23 17:54:56  brouard
   double f;    * 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.
   double *xt;  
      Revision 1.87  2003/06/18 12:26:01  brouard
   xt=vector(1,ncom);    Version 0.96
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);    Revision 1.86  2003/06/17 20:04:08  brouard
   free_vector(xt,1,ncom);    (Module): Change position of html and gnuplot routines and added
   return f;    routine fileappend.
 }  
     Revision 1.85  2003/06/17 13:12:43  brouard
 /*****************brent *************************/    * imach.c (Repository): Check when date of death was earlier that
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    current date of interview. It may happen when the death was just
 {    prior to the death. In this case, dh was negative and likelihood
   int iter;    was wrong (infinity). We still send an "Error" but patch by
   double a,b,d,etemp;    assuming that the date of death was just one stepm after the
   double fu,fv,fw,fx;    interview.
   double ftemp;    (Repository): Because some people have very long ID (first column)
   double p,q,r,tol1,tol2,u,v,w,x,xm;    we changed int to long in num[] and we added a new lvector for
   double e=0.0;    memory allocation. But we also truncated to 8 characters (left
      truncation)
   a=(ax < cx ? ax : cx);    (Repository): No more line truncation errors.
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    Revision 1.84  2003/06/13 21:44:43  brouard
   fw=fv=fx=(*f)(x);    * imach.c (Repository): Replace "freqsummary" at a correct
   for (iter=1;iter<=ITMAX;iter++) {    place. It differs from routine "prevalence" which may be called
     xm=0.5*(a+b);    many times. Probs is memory consuming and must be used with
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    parcimony.
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
     printf(".");fflush(stdout);  
 #ifdef DEBUG    Revision 1.83  2003/06/10 13:39:11  lievre
     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);    *** empty log message ***
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif    Revision 1.82  2003/06/05 15:57:20  brouard
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    Add log in  imach.c and  fullversion number is now printed.
       *xmin=x;  
       return fx;  */
     }  /*
     ftemp=fu;     Interpolated Markov Chain
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);    Short summary of the programme:
       q=(x-v)*(fx-fw);    
       p=(x-v)*q-(x-w)*r;    This program computes Healthy Life Expectancies from
       q=2.0*(q-r);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
       if (q > 0.0) p = -p;    first survey ("cross") where individuals from different ages are
       q=fabs(q);    interviewed on their health status or degree of disability (in the
       etemp=e;    case of a health survey which is our main interest) -2- at least a
       e=d;    second wave of interviews ("longitudinal") which measure each change
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    (if any) in individual health status.  Health expectancies are
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    computed from the time spent in each health state according to a
       else {    model. More health states you consider, more time is necessary to reach the
         d=p/q;    Maximum Likelihood of the parameters involved in the model.  The
         u=x+d;    simplest model is the multinomial logistic model where pij is the
         if (u-a < tol2 || b-u < tol2)    probability to be observed in state j at the second wave
           d=SIGN(tol1,xm-x);    conditional to be observed in state i at the first wave. Therefore
       }    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     } else {    'age' is age and 'sex' is a covariate. If you want to have a more
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    complex model than "constant and age", you should modify the program
     }    where the markup *Covariates have to be included here again* invites
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    you to do it.  More covariates you add, slower the
     fu=(*f)(u);    convergence.
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;    The advantage of this computer programme, compared to a simple
       SHFT(v,w,x,u)    multinomial logistic model, is clear when the delay between waves is not
         SHFT(fv,fw,fx,fu)    identical for each individual. Also, if a individual missed an
         } else {    intermediate interview, the information is lost, but taken into
           if (u < x) a=u; else b=u;    account using an interpolation or extrapolation.  
           if (fu <= fw || w == x) {  
             v=w;    hPijx is the probability to be observed in state i at age x+h
             w=u;    conditional to the observed state i at age x. The delay 'h' can be
             fv=fw;    split into an exact number (nh*stepm) of unobserved intermediate
             fw=fu;    states. This elementary transition (by month, quarter,
           } else if (fu <= fv || v == x || v == w) {    semester or year) is modelled as a multinomial logistic.  The hPx
             v=u;    matrix is simply the matrix product of nh*stepm elementary matrices
             fv=fu;    and the contribution of each individual to the likelihood is simply
           }    hPijx.
         }  
   }    Also this programme outputs the covariance matrix of the parameters but also
   nrerror("Too many iterations in brent");    of the life expectancies. It also computes the period (stable) prevalence. 
   *xmin=x;    
   return fx;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 }             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
 /****************** mnbrak ***********************/    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    software can be distributed freely for non commercial use. Latest version
             double (*func)(double))    can be accessed at http://euroreves.ined.fr/imach .
 {  
   double ulim,u,r,q, dum;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   double fu;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
      
   *fa=(*func)(*ax);    **********************************************************************/
   *fb=(*func)(*bx);  /*
   if (*fb > *fa) {    main
     SHFT(dum,*ax,*bx,dum)    read parameterfile
       SHFT(dum,*fb,*fa,dum)    read datafile
       }    concatwav
   *cx=(*bx)+GOLD*(*bx-*ax);    freqsummary
   *fc=(*func)(*cx);    if (mle >= 1)
   while (*fb > *fc) {      mlikeli
     r=(*bx-*ax)*(*fb-*fc);    print results files
     q=(*bx-*cx)*(*fb-*fa);    if mle==1 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/       computes hessian
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    read end of parameter file: agemin, agemax, bage, fage, estepm
     ulim=(*bx)+GLIMIT*(*cx-*bx);        begin-prev-date,...
     if ((*bx-u)*(u-*cx) > 0.0) {    open gnuplot file
       fu=(*func)(u);    open html file
     } else if ((*cx-u)*(u-ulim) > 0.0) {    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
       fu=(*func)(u);     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
       if (fu < *fc) {                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      freexexit2 possible for memory heap.
           SHFT(*fb,*fc,fu,(*func)(u))  
           }    h Pij x                         | pij_nom  ficrestpij
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
       u=ulim;         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
       fu=(*func)(u);         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
       fu=(*func)(u);         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
     }    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
     SHFT(*ax,*bx,*cx,u)     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
       SHFT(*fa,*fb,*fc,fu)     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
       }  
 }    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 /*************** linmin ************************/    Variance-covariance of DFLE
     prevalence()
 int ncom;     movingaverage()
 double *pcom,*xicom;    varevsij() 
 double (*nrfunc)(double []);    if popbased==1 varevsij(,popbased)
      total life expectancies
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    Variance of period (stable) prevalence
 {   end
   double brent(double ax, double bx, double cx,  */
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  #define POWELL /* Instead of NLOPT */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));  #include <math.h>
   int j;  #include <stdio.h>
   double xx,xmin,bx,ax;  #include <stdlib.h>
   double fx,fb,fa;  #include <string.h>
    
   ncom=n;  #ifdef _WIN32
   pcom=vector(1,n);  #include <io.h>
   xicom=vector(1,n);  #else
   nrfunc=func;  #include <unistd.h>
   for (j=1;j<=n;j++) {  #endif
     pcom[j]=p[j];  
     xicom[j]=xi[j];  #include <limits.h>
   }  #include <sys/types.h>
   ax=0.0;  #include <sys/stat.h>
   xx=1.0;  #include <errno.h>
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* extern int errno; */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  /* #ifdef LINUX */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  /* #include <time.h> */
 #endif  /* #include "timeval.h" */
   for (j=1;j<=n;j++) {  /* #else */
     xi[j] *= xmin;  /* #include <sys/time.h> */
     p[j] += xi[j];  /* #endif */
   }  
   free_vector(xicom,1,n);  #include <time.h>
   free_vector(pcom,1,n);  
 }  #ifdef GSL
   #include <gsl/gsl_errno.h>
 /*************** powell ************************/  #include <gsl/gsl_multimin.h>
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #endif
             double (*func)(double []))  
 {  #ifdef NLOPT
   void linmin(double p[], double xi[], int n, double *fret,  #include <nlopt.h>
               double (*func)(double []));  typedef struct {
   int i,ibig,j;    double (* function)(double [] );
   double del,t,*pt,*ptt,*xit;  } myfunc_data ;
   double fp,fptt;  #endif
   double *xits;  
   pt=vector(1,n);  /* #include <libintl.h> */
   ptt=vector(1,n);  /* #define _(String) gettext (String) */
   xit=vector(1,n);  
   xits=vector(1,n);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];  #define GNUPLOTPROGRAM "gnuplot"
   for (*iter=1;;++(*iter)) {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     fp=(*fret);  #define FILENAMELENGTH 132
     ibig=0;  
     del=0.0;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
     printf("\n");  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  #define NINTERVMAX 8
       fptt=(*fret);  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
 #ifdef DEBUG  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
       printf("fret=%lf \n",*fret);  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
 #endif  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
       printf("%d",i);fflush(stdout);  #define MAXN 20000
       linmin(p,xit,n,fret,func);  #define YEARM 12. /**< Number of months per year */
       if (fabs(fptt-(*fret)) > del) {  #define AGESUP 130
         del=fabs(fptt-(*fret));  #define AGEBASE 40
         ibig=i;  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
       }  #ifdef _WIN32
 #ifdef DEBUG  #define DIRSEPARATOR '\\'
       printf("%d %.12e",i,(*fret));  #define CHARSEPARATOR "\\"
       for (j=1;j<=n;j++) {  #define ODIRSEPARATOR '/'
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #else
         printf(" x(%d)=%.12e",j,xit[j]);  #define DIRSEPARATOR '/'
       }  #define CHARSEPARATOR "/"
       for(j=1;j<=n;j++)  #define ODIRSEPARATOR '\\'
         printf(" p=%.12e",p[j]);  #endif
       printf("\n");  
 #endif  /* $Id$ */
     }  /* $State$ */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG  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)";
       int k[2],l;  char fullversion[]="$Revision$ $Date$"; 
       k[0]=1;  char strstart[80];
       k[1]=-1;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       printf("Max: %.12e",(*func)(p));  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
       for (j=1;j<=n;j++)  int nvar=0, nforce=0; /* Number of variables, number of forces */
         printf(" %.12e",p[j]);  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
       printf("\n");  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
       for(l=0;l<=1;l++) {  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
         for (j=1;j<=n;j++) {  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  int cptcovprodnoage=0; /**< Number of covariate products without age */   
         }  int cptcoveff=0; /* Total number of covariates to vary for printing results */
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  int cptcov=0; /* Working variable */
       }  int npar=NPARMAX;
 #endif  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
   int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       free_vector(xit,1,n);  int popbased=0;
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  int *wav; /* Number of waves for this individuual 0 is possible */
       free_vector(pt,1,n);  int maxwav=0; /* Maxim number of waves */
       return;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     }  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     for (j=1;j<=n;j++) {                     to the likelihood and the sum of weights (done by funcone)*/
       ptt[j]=2.0*p[j]-pt[j];  int mle=1, weightopt=0;
       xit[j]=p[j]-pt[j];  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       pt[j]=p[j];  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     }  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     fptt=(*func)(ptt);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     if (fptt < fp) {  int countcallfunc=0;  /* Count the number of calls to func */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  double jmean=1; /* Mean space between 2 waves */
       if (t < 0.0) {  double **matprod2(); /* test */
         linmin(p,xit,n,fret,func);  double **oldm, **newm, **savm; /* Working pointers to matrices */
         for (j=1;j<=n;j++) {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
           xi[j][ibig]=xi[j][n];  /*FILE *fic ; */ /* Used in readdata only */
           xi[j][n]=xit[j];  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
         }  FILE *ficlog, *ficrespow;
 #ifdef DEBUG  int globpr=0; /* Global variable for printing or not */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  double fretone; /* Only one call to likelihood */
         for(j=1;j<=n;j++)  long ipmx=0; /* Number of contributions */
           printf(" %.12e",xit[j]);  double sw; /* Sum of weights */
         printf("\n");  char filerespow[FILENAMELENGTH];
 #endif  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       }  FILE *ficresilk;
     }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   }  FILE *ficresprobmorprev;
 }  FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
 /**** Prevalence limit ****************/  char filerese[FILENAMELENGTH];
   FILE *ficresstdeij;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  char fileresstde[FILENAMELENGTH];
 {  FILE *ficrescveij;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  char filerescve[FILENAMELENGTH];
      matrix by transitions matrix until convergence is reached */  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
   int i, ii,j,k;  FILE  *ficresvpl;
   double min, max, maxmin, maxmax,sumnew=0.;  char fileresvpl[FILENAMELENGTH];
   double **matprod2();  char title[MAXLINE];
   double **out, cov[NCOVMAX], **pmij();  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   double **newm;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   double agefin, delaymax=50 ; /* Max number of years to converge */  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   char command[FILENAMELENGTH];
   for (ii=1;ii<=nlstate+ndeath;ii++)  int  outcmd=0;
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     }  
   char filelog[FILENAMELENGTH]; /* Log file */
    cov[1]=1.;  char filerest[FILENAMELENGTH];
    char fileregp[FILENAMELENGTH];
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  char popfile[FILENAMELENGTH];
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     /* Covariates have to be included here again */  
      cov[2]=agefin;  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
    /* struct timezone tzp; */
       for (k=1; k<=cptcovn;k++) {  /* extern int gettimeofday(); */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  struct tm tml, *gmtime(), *localtime();
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  
       }  extern time_t time();
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  struct tm start_time, end_time, curr_time, last_time, forecast_time;
       for (k=1; k<=cptcovprod;k++)  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  struct tm tm;
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  char strcurr[80], strfor[80];
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
   char *endptr;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  long lval;
   double dval;
     savm=oldm;  
     oldm=newm;  #define NR_END 1
     maxmax=0.;  #define FREE_ARG char*
     for(j=1;j<=nlstate;j++){  #define FTOL 1.0e-10
       min=1.;  
       max=0.;  #define NRANSI 
       for(i=1; i<=nlstate; i++) {  #define ITMAX 200 
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  #define TOL 2.0e-4 
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  #define CGOLD 0.3819660 
         min=FMIN(min,prlim[i][j]);  #define ZEPS 1.0e-10 
       }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       maxmin=max-min;  
       maxmax=FMAX(maxmax,maxmin);  #define GOLD 1.618034 
     }  #define GLIMIT 100.0 
     if(maxmax < ftolpl){  #define TINY 1.0e-20 
       return prlim;  
     }  static double maxarg1,maxarg2;
   }  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 }  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     
 /*************** transition probabilities ***************/  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  static double sqrarg;
   double s1, s2;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   /*double t34;*/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int i,j,j1, nc, ii, jj;  int agegomp= AGEGOMP;
   
     for(i=1; i<= nlstate; i++){  int imx; 
     for(j=1; j<i;j++){  int stepm=1;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /* Stepm, step in month: minimum step interpolation*/
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  int estepm;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       }  
       ps[i][j]=s2;  int m,nb;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  long *num;
     }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     for(j=i+1; j<=nlstate+ndeath;j++){  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  double **pmmij, ***probs;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  double *ageexmed,*agecens;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  double dateintmean=0;
       }  
       ps[i][j]=(s2);  double *weight;
     }  int **s; /* Status */
   }  double *agedc;
     /*ps[3][2]=1;*/  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
                     * covar=matrix(0,NCOVMAX,1,n); 
   for(i=1; i<= nlstate; i++){                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
      s1=0;  double  idx; 
     for(j=1; j<i; j++)  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
       s1+=exp(ps[i][j]);  int *Ndum; /** Freq of modality (tricode */
     for(j=i+1; j<=nlstate+ndeath; j++)  int **codtab; /**< codtab=imatrix(1,100,1,10); */
       s1+=exp(ps[i][j]);  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
     ps[i][i]=1./(s1+1.);  double *lsurv, *lpop, *tpop;
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
     for(j=i+1; j<=nlstate+ndeath; j++)  double ftolhess; /**< Tolerance for computing hessian */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  /**************** split *************************/
   } /* end i */  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     for(jj=1; jj<= nlstate+ndeath; jj++){       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       ps[ii][jj]=0;    */ 
       ps[ii][ii]=1;    char  *ss;                            /* pointer */
     }    int   l1, l2;                         /* length counters */
   }  
     l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     for(jj=1; jj<= nlstate+ndeath; jj++){    if ( ss == NULL ) {                   /* no directory, so determine current directory */
      printf("%lf ",ps[ii][jj]);      strcpy( name, path );               /* we got the fullname name because no directory */
    }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     printf("\n ");        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     }      /* get current working directory */
     printf("\n ");printf("%lf ",cov[2]);*/      /*    extern  char* getcwd ( char *buf , int len);*/
 /*      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        return( GLOCK_ERROR_GETCWD );
   goto end;*/      }
     return ps;      /* got dirc from getcwd*/
 }      printf(" DIRC = %s \n",dirc);
     } else {                              /* strip direcotry from path */
 /**************** Product of 2 matrices ******************/      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 {      strcpy( name, ss );         /* save file name */
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      strncpy( dirc, path, l1 - l2 );     /* now the directory */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      dirc[l1-l2] = 0;                    /* add zero */
   /* in, b, out are matrice of pointers which should have been initialized      printf(" DIRC2 = %s \n",dirc);
      before: only the contents of out is modified. The function returns    }
      a pointer to pointers identical to out */    /* We add a separator at the end of dirc if not exists */
   long i, j, k;    l1 = strlen( dirc );                  /* length of directory */
   for(i=nrl; i<= nrh; i++)    if( dirc[l1-1] != DIRSEPARATOR ){
     for(k=ncolol; k<=ncoloh; k++)      dirc[l1] =  DIRSEPARATOR;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      dirc[l1+1] = 0; 
         out[i][k] +=in[i][j]*b[j][k];      printf(" DIRC3 = %s \n",dirc);
     }
   return out;    ss = strrchr( name, '.' );            /* find last / */
 }    if (ss >0){
       ss++;
       strcpy(ext,ss);                     /* save extension */
 /************* Higher Matrix Product ***************/      l1= strlen( name);
       l2= strlen(ss)+1;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      strncpy( finame, name, l1-l2);
 {      finame[l1-l2]= 0;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    }
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    return( 0 );                          /* we're done */
      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).  
      Model is determined by parameters x and covariates have to be  
      included manually here.  /******************************************/
   
      */  void replace_back_to_slash(char *s, char*t)
   {
   int i, j, d, h, k;    int i;
   double **out, cov[NCOVMAX];    int lg=0;
   double **newm;    i=0;
     lg=strlen(t);
   /* Hstepm could be zero and should return the unit matrix */    for(i=0; i<= lg; i++) {
   for (i=1;i<=nlstate+ndeath;i++)      (s[i] = t[i]);
     for (j=1;j<=nlstate+ndeath;j++){      if (t[i]== '\\') s[i]='/';
       oldm[i][j]=(i==j ? 1.0 : 0.0);    }
       po[i][j][0]=(i==j ? 1.0 : 0.0);  }
     }  
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  char *trimbb(char *out, char *in)
   for(h=1; h <=nhstepm; h++){  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     for(d=1; d <=hstepm; d++){    char *s;
       newm=savm;    s=out;
       /* Covariates have to be included here again */    while (*in != '\0'){
       cov[1]=1.;      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        in++;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      }
       for (k=1; k<=cptcovage;k++)      *out++ = *in++;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    }
       for (k=1; k<=cptcovprod;k++)    *out='\0';
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    return s;
   }
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  char *cutl(char *blocc, char *alocc, char *in, char occ)
       /*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,    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       savm=oldm;       gives blocc="abcdef2ghi" and alocc="j".
       oldm=newm;       If occ is not found blocc is null and alocc is equal to in. Returns blocc
     }    */
     for(i=1; i<=nlstate+ndeath; i++)    char *s, *t;
       for(j=1;j<=nlstate+ndeath;j++) {    t=in;s=in;
         po[i][j][h]=newm[i][j];    while ((*in != occ) && (*in != '\0')){
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      *alocc++ = *in++;
          */    }
       }    if( *in == occ){
   } /* end h */      *(alocc)='\0';
   return po;      s=++in;
 }    }
    
     if (s == t) {/* occ not found */
 /*************** log-likelihood *************/      *(alocc-(in-s))='\0';
 double func( double *x)      in=s;
 {    }
   int i, ii, j, k, mi, d, kk;    while ( *in != '\0'){
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      *blocc++ = *in++;
   double **out;    }
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */    *blocc='\0';
   long ipmx;    return t;
   /*extern weight */  }
   /* We are differentiating ll according to initial status */  char *cutv(char *blocc, char *alocc, char *in, char occ)
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  {
   /*for(i=1;i<imx;i++)    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
     printf(" %d\n",s[4][i]);       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   */       gives blocc="abcdef2ghi" and alocc="j".
   cov[1]=1.;       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     */
   for(k=1; k<=nlstate; k++) ll[k]=0.;    char *s, *t;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    t=in;s=in;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    while (*in != '\0'){
     for(mi=1; mi<= wav[i]-1; mi++){      while( *in == occ){
       for (ii=1;ii<=nlstate+ndeath;ii++)        *blocc++ = *in++;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        s=in;
       for(d=0; d<dh[mi][i]; d++){      }
         newm=savm;      *blocc++ = *in++;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    }
         for (kk=1; kk<=cptcovage;kk++) {    if (s == t) /* occ not found */
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      *(blocc-(in-s))='\0';
         }    else
              *(blocc-(in-s)-1)='\0';
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    in=s;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    while ( *in != '\0'){
         savm=oldm;      *alocc++ = *in++;
         oldm=newm;    }
          
            *alocc='\0';
       } /* end mult */    return s;
        }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  int nbocc(char *s, char occ)
       ipmx +=1;  {
       sw += weight[i];    int i,j=0;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    int lg=20;
     } /* end of wave */    i=0;
   } /* end of individual */    lg=strlen(s);
     for(i=0; i<= lg; i++) {
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    if  (s[i] == occ ) j++;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    }
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    return j;
   return -l;  }
 }  
   /* void cutv(char *u,char *v, char*t, char occ) */
   /* { */
 /*********** Maximum Likelihood Estimation ***************/  /*   /\* 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') */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  /*      gives u="abcdef2ghi" and v="j" *\/ */
 {  /*   int i,lg,j,p=0; */
   int i,j, iter;  /*   i=0; */
   double **xi,*delti;  /*   lg=strlen(t); */
   double fret;  /*   for(j=0; j<=lg-1; j++) { */
   xi=matrix(1,npar,1,npar);  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   for (i=1;i<=npar;i++)  /*   } */
     for (j=1;j<=npar;j++)  
       xi[i][j]=(i==j ? 1.0 : 0.0);  /*   for(j=0; j<p; j++) { */
   printf("Powell\n");  /*     (u[j] = t[j]); */
   powell(p,xi,npar,ftol,&iter,&fret,func);  /*   } */
   /*      u[p]='\0'; */
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));  /*    for(j=0; j<= lg; j++) { */
   /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
 }  /*   } */
   /* } */
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  #ifdef _WIN32
 {  char * strsep(char **pp, const char *delim)
   double  **a,**y,*x,pd;  {
   double **hess;    char *p, *q;
   int i, j,jk;           
   int *indx;    if ((p = *pp) == NULL)
       return 0;
   double hessii(double p[], double delta, int theta, double delti[]);    if ((q = strpbrk (p, delim)) != NULL)
   double hessij(double p[], double delti[], int i, int j);    {
   void lubksb(double **a, int npar, int *indx, double b[]) ;      *pp = q + 1;
   void ludcmp(double **a, int npar, int *indx, double *d) ;      *q = '\0';
     }
   hess=matrix(1,npar,1,npar);    else
       *pp = 0;
   printf("\nCalculation of the hessian matrix. Wait...\n");    return p;
   for (i=1;i<=npar;i++){  }
     printf("%d",i);fflush(stdout);  #endif
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/  /********************** nrerror ********************/
     /*printf(" %lf ",hess[i][i]);*/  
   }  void nrerror(char error_text[])
    {
   for (i=1;i<=npar;i++) {    fprintf(stderr,"ERREUR ...\n");
     for (j=1;j<=npar;j++)  {    fprintf(stderr,"%s\n",error_text);
       if (j>i) {    exit(EXIT_FAILURE);
         printf(".%d%d",i,j);fflush(stdout);  }
         hess[i][j]=hessij(p,delti,i,j);  /*********************** vector *******************/
         hess[j][i]=hess[i][j];      double *vector(int nl, int nh)
         /*printf(" %lf ",hess[i][j]);*/  {
       }    double *v;
     }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   }    if (!v) nrerror("allocation failure in vector");
   printf("\n");    return v-nl+NR_END;
   }
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  
    /************************ free vector ******************/
   a=matrix(1,npar,1,npar);  void free_vector(double*v, int nl, int nh)
   y=matrix(1,npar,1,npar);  {
   x=vector(1,npar);    free((FREE_ARG)(v+nl-NR_END));
   indx=ivector(1,npar);  }
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  /************************ivector *******************************/
   ludcmp(a,npar,indx,&pd);  int *ivector(long nl,long nh)
   {
   for (j=1;j<=npar;j++) {    int *v;
     for (i=1;i<=npar;i++) x[i]=0;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     x[j]=1;    if (!v) nrerror("allocation failure in ivector");
     lubksb(a,npar,indx,x);    return v-nl+NR_END;
     for (i=1;i<=npar;i++){  }
       matcov[i][j]=x[i];  
     }  /******************free ivector **************************/
   }  void free_ivector(int *v, long nl, long nh)
   {
   printf("\n#Hessian matrix#\n");    free((FREE_ARG)(v+nl-NR_END));
   for (i=1;i<=npar;i++) {  }
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);  /************************lvector *******************************/
     }  long *lvector(long nl,long nh)
     printf("\n");  {
   }    long *v;
     v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   /* Recompute Inverse */    if (!v) nrerror("allocation failure in ivector");
   for (i=1;i<=npar;i++)    return v-nl+NR_END;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  }
   ludcmp(a,npar,indx,&pd);  
   /******************free lvector **************************/
   /*  printf("\n#Hessian matrix recomputed#\n");  void free_lvector(long *v, long nl, long nh)
   {
   for (j=1;j<=npar;j++) {    free((FREE_ARG)(v+nl-NR_END));
     for (i=1;i<=npar;i++) x[i]=0;  }
     x[j]=1;  
     lubksb(a,npar,indx,x);  /******************* imatrix *******************************/
     for (i=1;i<=npar;i++){  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       y[i][j]=x[i];       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       printf("%.3e ",y[i][j]);  { 
     }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     printf("\n");    int **m; 
   }    
   */    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   free_matrix(a,1,npar,1,npar);    if (!m) nrerror("allocation failure 1 in matrix()"); 
   free_matrix(y,1,npar,1,npar);    m += NR_END; 
   free_vector(x,1,npar);    m -= nrl; 
   free_ivector(indx,1,npar);    
   free_matrix(hess,1,npar,1,npar);    
     /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
 /*************** hessian matrix ****************/    m[nrl] -= ncl; 
 double hessii( double x[], double delta, int theta, double delti[])    
 {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   int i;    
   int l=1, lmax=20;    /* return pointer to array of pointers to rows */ 
   double k1,k2;    return m; 
   double p2[NPARMAX+1];  } 
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  /****************** free_imatrix *************************/
   double fx;  void free_imatrix(m,nrl,nrh,ncl,nch)
   int k=0,kmax=10;        int **m;
   double l1;        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
   fx=func(x);  { 
   for (i=1;i<=npar;i++) p2[i]=x[i];    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   for(l=0 ; l <=lmax; l++){    free((FREE_ARG) (m+nrl-NR_END)); 
     l1=pow(10,l);  } 
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){  /******************* matrix *******************************/
       delt = delta*(l1*k);  double **matrix(long nrl, long nrh, long ncl, long nch)
       p2[theta]=x[theta] +delt;  {
       k1=func(p2)-fx;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       p2[theta]=x[theta]-delt;    double **m;
       k2=func(p2)-fx;  
       /*res= (k1-2.0*fx+k2)/delt/delt; */    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    if (!m) nrerror("allocation failure 1 in matrix()");
          m += NR_END;
 #ifdef DEBUG    m -= nrl;
       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    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    m[nrl] += NR_END;
         k=kmax;    m[nrl] -= ncl;
       }  
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         k=kmax; l=lmax*10.;    return m;
       }    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
         delts=delt;  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
       }     */
     }  }
   }  
   delti[theta]=delts;  /*************************free matrix ************************/
   return res;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
    {
 }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 double hessij( double x[], double delti[], int thetai,int thetaj)  }
 {  
   int i;  /******************* ma3x *******************************/
   int l=1, l1, lmax=20;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   double k1,k2,k3,k4,res,fx;  {
   double p2[NPARMAX+1];    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   int k;    double ***m;
   
   fx=func(x);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   for (k=1; k<=2; k++) {    if (!m) nrerror("allocation failure 1 in matrix()");
     for (i=1;i<=npar;i++) p2[i]=x[i];    m += NR_END;
     p2[thetai]=x[thetai]+delti[thetai]/k;    m -= nrl;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     p2[thetai]=x[thetai]+delti[thetai]/k;    m[nrl] += NR_END;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    m[nrl] -= ncl;
     k2=func(p2)-fx;  
      for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     k3=func(p2)-fx;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
      m[nrl][ncl] += NR_END;
     p2[thetai]=x[thetai]-delti[thetai]/k;    m[nrl][ncl] -= nll;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    for (j=ncl+1; j<=nch; j++) 
     k4=func(p2)-fx;      m[nrl][j]=m[nrl][j-1]+nlay;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    
 #ifdef DEBUG    for (i=nrl+1; i<=nrh; i++) {
     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);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 #endif      for (j=ncl+1; j<=nch; j++) 
   }        m[i][j]=m[i][j-1]+nlay;
   return res;    }
 }    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 /************** Inverse of matrix **************/             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 void ludcmp(double **a, int n, int *indx, double *d)    */
 {  }
   int i,imax,j,k;  
   double big,dum,sum,temp;  /*************************free ma3x ************************/
   double *vv;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
    {
   vv=vector(1,n);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   *d=1.0;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for (i=1;i<=n;i++) {    free((FREE_ARG)(m+nrl-NR_END));
     big=0.0;  }
     for (j=1;j<=n;j++)  
       if ((temp=fabs(a[i][j])) > big) big=temp;  /*************** function subdirf ***********/
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  char *subdirf(char fileres[])
     vv[i]=1.0/big;  {
   }    /* Caution optionfilefiname is hidden */
   for (j=1;j<=n;j++) {    strcpy(tmpout,optionfilefiname);
     for (i=1;i<j;i++) {    strcat(tmpout,"/"); /* Add to the right */
       sum=a[i][j];    strcat(tmpout,fileres);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    return tmpout;
       a[i][j]=sum;  }
     }  
     big=0.0;  /*************** function subdirf2 ***********/
     for (i=j;i<=n;i++) {  char *subdirf2(char fileres[], char *preop)
       sum=a[i][j];  {
       for (k=1;k<j;k++)    
         sum -= a[i][k]*a[k][j];    /* Caution optionfilefiname is hidden */
       a[i][j]=sum;    strcpy(tmpout,optionfilefiname);
       if ( (dum=vv[i]*fabs(sum)) >= big) {    strcat(tmpout,"/");
         big=dum;    strcat(tmpout,preop);
         imax=i;    strcat(tmpout,fileres);
       }    return tmpout;
     }  }
     if (j != imax) {  
       for (k=1;k<=n;k++) {  /*************** function subdirf3 ***********/
         dum=a[imax][k];  char *subdirf3(char fileres[], char *preop, char *preop2)
         a[imax][k]=a[j][k];  {
         a[j][k]=dum;    
       }    /* Caution optionfilefiname is hidden */
       *d = -(*d);    strcpy(tmpout,optionfilefiname);
       vv[imax]=vv[j];    strcat(tmpout,"/");
     }    strcat(tmpout,preop);
     indx[j]=imax;    strcat(tmpout,preop2);
     if (a[j][j] == 0.0) a[j][j]=TINY;    strcat(tmpout,fileres);
     if (j != n) {    return tmpout;
       dum=1.0/(a[j][j]);  }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }  char *asc_diff_time(long time_sec, char ascdiff[])
   }  {
   free_vector(vv,1,n);  /* Doesn't work */    long sec_left, days, hours, minutes;
 ;    days = (time_sec) / (60*60*24);
 }    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
 void lubksb(double **a, int n, int *indx, double b[])    sec_left = (sec_left) %(60*60);
 {    minutes = (sec_left) /60;
   int i,ii=0,ip,j;    sec_left = (sec_left) % (60);
   double sum;    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
      return ascdiff;
   for (i=1;i<=n;i++) {  }
     ip=indx[i];  
     sum=b[ip];  /***************** f1dim *************************/
     b[ip]=b[i];  extern int ncom; 
     if (ii)  extern double *pcom,*xicom;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  extern double (*nrfunc)(double []); 
     else if (sum) ii=i;   
     b[i]=sum;  double f1dim(double x) 
   }  { 
   for (i=n;i>=1;i--) {    int j; 
     sum=b[i];    double f;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    double *xt; 
     b[i]=sum/a[i][i];   
   }    xt=vector(1,ncom); 
 }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
 /************ Frequencies ********************/    free_vector(xt,1,ncom); 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)    return f; 
 {  /* Some frequencies */  } 
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  /*****************brent *************************/
   double ***freq; /* Frequencies */  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   double *pp;  { 
   double pos;    int iter; 
   FILE *ficresp;    double a,b,d,etemp;
   char fileresp[FILENAMELENGTH];    double fu=0,fv,fw,fx;
     double ftemp=0.;
   pp=vector(1,nlstate);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
   strcpy(fileresp,"p");   
   strcat(fileresp,fileres);    a=(ax < cx ? ax : cx); 
   if((ficresp=fopen(fileresp,"w"))==NULL) {    b=(ax > cx ? ax : cx); 
     printf("Problem with prevalence resultfile: %s\n", fileresp);    x=w=v=bx; 
     exit(0);    fw=fv=fx=(*f)(x); 
   }    for (iter=1;iter<=ITMAX;iter++) { 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      xm=0.5*(a+b); 
   j1=0;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   j=cptcoveff;      printf(".");fflush(stdout);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUGBRENT
   for(k1=1; k1<=j;k1++){      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
    for(i1=1; i1<=ncodemax[k1];i1++){      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);
        j1++;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  #endif
          scanf("%d", i);*/      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         for (i=-1; i<=nlstate+ndeath; i++)          *xmin=x; 
          for (jk=-1; jk<=nlstate+ndeath; jk++)          return fx; 
            for(m=agemin; m <= agemax+3; m++)      } 
              freq[i][jk][m]=0;      ftemp=fu;
              if (fabs(e) > tol1) { 
        for (i=1; i<=imx; i++) {        r=(x-w)*(fx-fv); 
          bool=1;        q=(x-v)*(fx-fw); 
          if  (cptcovn>0) {        p=(x-v)*q-(x-w)*r; 
            for (z1=1; z1<=cptcoveff; z1++)        q=2.0*(q-r); 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        if (q > 0.0) p = -p; 
                bool=0;        q=fabs(q); 
          }        etemp=e; 
           if (bool==1) {        e=d; 
            for(m=firstpass; m<=lastpass-1; m++){        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
              if(agev[m][i]==0) agev[m][i]=agemax+1;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
              if(agev[m][i]==1) agev[m][i]=agemax+2;        else { 
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          d=p/q; 
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          u=x+d; 
            }          if (u-a < tol2 || b-u < tol2) 
          }            d=SIGN(tol1,xm-x); 
        }        } 
         if  (cptcovn>0) {      } else { 
          fprintf(ficresp, "\n#********** Variable ");        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      } 
        fprintf(ficresp, "**********\n#");      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         }      fu=(*f)(u); 
        for(i=1; i<=nlstate;i++)      if (fu <= fx) { 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        if (u >= x) a=x; else b=x; 
        fprintf(ficresp, "\n");        SHFT(v,w,x,u) 
                  SHFT(fv,fw,fx,fu) 
   for(i=(int)agemin; i <= (int)agemax+3; i++){          } else { 
     if(i==(int)agemax+3)            if (u < x) a=u; else b=u; 
       printf("Total");            if (fu <= fw || w == x) { 
     else              v=w; 
       printf("Age %d", i);              w=u; 
     for(jk=1; jk <=nlstate ; jk++){              fv=fw; 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              fw=fu; 
         pp[jk] += freq[jk][m][i];            } else if (fu <= fv || v == x || v == w) { 
     }              v=u; 
     for(jk=1; jk <=nlstate ; jk++){              fv=fu; 
       for(m=-1, pos=0; m <=0 ; m++)            } 
         pos += freq[jk][m][i];          } 
       if(pp[jk]>=1.e-10)    } 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    nrerror("Too many iterations in brent"); 
       else    *xmin=x; 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    return fx; 
     }  } 
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)  /****************** mnbrak ***********************/
         pp[jk] += freq[jk][m][i];  
     }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     for(jk=1,pos=0; jk <=nlstate ; jk++)              double (*func)(double)) 
       pos += pp[jk];  { 
     for(jk=1; jk <=nlstate ; jk++){    double ulim,u,r,q, dum;
       if(pos>=1.e-5)    double fu; 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);   
       else    *fa=(*func)(*ax); 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    *fb=(*func)(*bx); 
       if( i <= (int) agemax){    if (*fb > *fa) { 
         if(pos>=1.e-5)      SHFT(dum,*ax,*bx,dum) 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        SHFT(dum,*fb,*fa,dum) 
       else        } 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    *cx=(*bx)+GOLD*(*bx-*ax); 
       }    *fc=(*func)(*cx); 
     }    while (*fb > *fc) { /* Declining fa, fb, fc */
     for(jk=-1; jk <=nlstate+ndeath; jk++)      r=(*bx-*ax)*(*fb-*fc); 
       for(m=-1; m <=nlstate+ndeath; m++)      q=(*bx-*cx)*(*fb-*fa); 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     if(i <= (int) agemax)        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
       fprintf(ficresp,"\n");      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
     printf("\n");      if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
     }        fu=(*func)(u); 
     }  #ifdef DEBUG
  }        /* f(x)=A(x-u)**2+f(u) */
          double A, fparabu; 
   fclose(ficresp);        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        fparabu= *fa - A*(*ax-u)*(*ax-u);
   free_vector(pp,1,nlstate);        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);
         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);
 }  /* End of Freq */  #endif 
       } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
 /************* Waves Concatenation ***************/        fu=(*func)(u); 
         if (fu < *fc) { 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 {            SHFT(*fb,*fc,fu,(*func)(u)) 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            } 
      Death is a valid wave (if date is known).      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        u=ulim; 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        fu=(*func)(u); 
      and mw[mi+1][i]. dh depends on stepm.      } else { 
      */        u=(*cx)+GOLD*(*cx-*bx); 
         fu=(*func)(u); 
   int i, mi, m;      } 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      SHFT(*ax,*bx,*cx,u) 
      double sum=0., jmean=0.;*/        SHFT(*fa,*fb,*fc,fu) 
         } 
   int j, k=0,jk, ju, jl;  } 
   double sum=0.;  
   jmin=1e+5;  /*************** linmin ************************/
   jmax=-1;  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
   jmean=0.;  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
   for(i=1; i<=imx; i++){  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
     mi=0;  the value of func at the returned location p . This is actually all accomplished by calling the
     m=firstpass;  routines mnbrak and brent .*/
     while(s[m][i] <= nlstate){  int ncom; 
       if(s[m][i]>=1)  double *pcom,*xicom;
         mw[++mi][i]=m;  double (*nrfunc)(double []); 
       if(m >=lastpass)   
         break;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       else  { 
         m++;    double brent(double ax, double bx, double cx, 
     }/* end while */                 double (*f)(double), double tol, double *xmin); 
     if (s[m][i] > nlstate){    double f1dim(double x); 
       mi++;     /* Death is another wave */    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       /* if(mi==0)  never been interviewed correctly before death */                double *fc, double (*func)(double)); 
          /* Only death is a correct wave */    int j; 
       mw[mi][i]=m;    double xx,xmin,bx,ax; 
     }    double fx,fb,fa;
    
     wav[i]=mi;    ncom=n; 
     if(mi==0)    pcom=vector(1,n); 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    xicom=vector(1,n); 
   }    nrfunc=func; 
     for (j=1;j<=n;j++) { 
   for(i=1; i<=imx; i++){      pcom[j]=p[j]; 
     for(mi=1; mi<wav[i];mi++){      xicom[j]=xi[j]; 
       if (stepm <=0)    } 
         dh[mi][i]=1;    ax=0.0; 
       else{    xx=1.0; 
         if (s[mw[mi+1][i]][i] > nlstate) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
           if (agedc[i] < 2*AGESUP) {    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  #ifdef DEBUG
           if(j==0) j=1;  /* Survives at least one month after exam */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
           k=k+1;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
           if (j >= jmax) jmax=j;  #endif
           if (j <= jmin) jmin=j;    for (j=1;j<=n;j++) { 
           sum=sum+j;      xi[j] *= xmin; 
           /* if (j<10) printf("j=%d num=%d ",j,i); */      p[j] += xi[j]; 
           }    } 
         }    free_vector(xicom,1,n); 
         else{    free_vector(pcom,1,n); 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  } 
           k=k+1;  
           if (j >= jmax) jmax=j;  
           else if (j <= jmin)jmin=j;  /*************** powell ************************/
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  /*
           sum=sum+j;  Minimization of a function func of n variables. Input consists of an initial starting point
         }  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
         jk= j/stepm;  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
         jl= j -jk*stepm;  such that failure to decrease by more than this amount on one iteration signals doneness. On
         ju= j -(jk+1)*stepm;  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
         if(jl <= -ju)  function value at p , and iter is the number of iterations taken. The routine linmin is used.
           dh[mi][i]=jk;   */
         else  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
           dh[mi][i]=jk+1;              double (*func)(double [])) 
         if(dh[mi][i]==0)  { 
           dh[mi][i]=1; /* At least one step */    void linmin(double p[], double xi[], int n, double *fret, 
       }                double (*func)(double [])); 
     }    int i,ibig,j; 
   }    double del,t,*pt,*ptt,*xit;
   jmean=sum/k;    double fp,fptt;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    double *xits;
  }    int niterf, itmp;
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)    pt=vector(1,n); 
 {    ptt=vector(1,n); 
   int Ndum[20],ij=1, k, j, i;    xit=vector(1,n); 
   int cptcode=0;    xits=vector(1,n); 
   cptcoveff=0;    *fret=(*func)(p); 
      for (j=1;j<=n;j++) pt[j]=p[j]; 
   for (k=0; k<19; k++) Ndum[k]=0;      rcurr_time = time(NULL);  
   for (k=1; k<=7; k++) ncodemax[k]=0;    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      ibig=0; 
     for (i=1; i<=imx; i++) {      del=0.0; 
       ij=(int)(covar[Tvar[j]][i]);      rlast_time=rcurr_time;
       Ndum[ij]++;      /* (void) gettimeofday(&curr_time,&tzp); */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      rcurr_time = time(NULL);  
       if (ij > cptcode) cptcode=ij;      curr_time = *localtime(&rcurr_time);
     }      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 (i=0; i<=cptcode; i++) {  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
       if(Ndum[i]!=0) ncodemax[j]++;     for (i=1;i<=n;i++) {
     }        printf(" %d %.12f",i, p[i]);
     ij=1;        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
       }
     for (i=1; i<=ncodemax[j]; i++) {      printf("\n");
       for (k=0; k<=19; k++) {      fprintf(ficlog,"\n");
         if (Ndum[k] != 0) {      fprintf(ficrespow,"\n");fflush(ficrespow);
           nbcode[Tvar[j]][ij]=k;      if(*iter <=3){
           ij++;        tml = *localtime(&rcurr_time);
         }        strcpy(strcurr,asctime(&tml));
         if (ij > ncodemax[j]) break;        rforecast_time=rcurr_time; 
       }          itmp = strlen(strcurr);
     }        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   }            strcurr[itmp-1]='\0';
         printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
  for (k=0; k<19; k++) Ndum[k]=0;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
         for(niterf=10;niterf<=30;niterf+=10){
  for (i=1; i<=ncovmodel-2; i++) {          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
       ij=Tvar[i];          forecast_time = *localtime(&rforecast_time);
       Ndum[ij]++;          strcpy(strfor,asctime(&forecast_time));
     }          itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
  ij=1;          strfor[itmp-1]='\0';
  for (i=1; i<=10; 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);
    if((Ndum[i]!=0) && (i<=ncov)){          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);
      Tvaraff[ij]=i;        }
      ij++;      }
    }      for (i=1;i<=n;i++) { 
  }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
          fptt=(*fret); 
     cptcoveff=ij-1;  #ifdef DEBUG
 }            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
             fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
 /*********** Health Expectancies ****************/  #endif
         printf("%d",i);fflush(stdout);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        fprintf(ficlog,"%d",i);fflush(ficlog);
 {        linmin(p,xit,n,fret,func); 
   /* Health expectancies */        if (fabs(fptt-(*fret)) > del) { 
   int i, j, nhstepm, hstepm, h;          del=fabs(fptt-(*fret)); 
   double age, agelim,hf;          ibig=i; 
   double ***p3mat;        } 
    #ifdef DEBUG
   fprintf(ficreseij,"# Health expectancies\n");        printf("%d %.12e",i,(*fret));
   fprintf(ficreseij,"# Age");        fprintf(ficlog,"%d %.12e",i,(*fret));
   for(i=1; i<=nlstate;i++)        for (j=1;j<=n;j++) {
     for(j=1; j<=nlstate;j++)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       fprintf(ficreseij," %1d-%1d",i,j);          printf(" x(%d)=%.12e",j,xit[j]);
   fprintf(ficreseij,"\n");          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
   hstepm=1*YEARM; /*  Every j years of age (in month) */        for(j=1;j<=n;j++) {
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          printf(" p(%d)=%.12e",j,p[j]);
           fprintf(ficlog," p(%d)=%.12e",j,p[j]);
   agelim=AGESUP;        }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        printf("\n");
     /* nhstepm age range expressed in number of stepm */        fprintf(ficlog,"\n");
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  #endif
     /* Typically if 20 years = 20*12/6=40 stepm */      } /* end i */
     if (stepm >= YEARM) hstepm=1;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */  #ifdef DEBUG
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        int k[2],l;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        k[0]=1;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        k[1]=-1;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
     for(i=1; i<=nlstate;i++)          printf(" %.12e",p[j]);
       for(j=1; j<=nlstate;j++)          fprintf(ficlog," %.12e",p[j]);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){        }
           eij[i][j][(int)age] +=p3mat[i][j][h];        printf("\n");
         }        fprintf(ficlog,"\n");
            for(l=0;l<=1;l++) {
     hf=1;          for (j=1;j<=n;j++) {
     if (stepm >= YEARM) hf=stepm/YEARM;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     fprintf(ficreseij,"%.0f",age );            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     for(i=1; i<=nlstate;i++)            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for(j=1; j<=nlstate;j++){          }
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     fprintf(ficreseij,"\n");        }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  #endif
   }  
 }  
         free_vector(xit,1,n); 
 /************ Variance ******************/        free_vector(xits,1,n); 
 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)        free_vector(ptt,1,n); 
 {        free_vector(pt,1,n); 
   /* Variance of health expectancies */        return; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      } 
   double **newm;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   double **dnewm,**doldm;      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
   int i, j, nhstepm, hstepm, h;        ptt[j]=2.0*p[j]-pt[j]; 
   int k, cptcode;        xit[j]=p[j]-pt[j]; 
   double *xp;        pt[j]=p[j]; 
   double **gp, **gm;      } 
   double ***gradg, ***trgradg;      fptt=(*func)(ptt); 
   double ***p3mat;      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
   double age,agelim;        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
   int theta;        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
         /* Let f"(x2) be the 2nd derivative equal everywhere.  */
    fprintf(ficresvij,"# Covariances of life expectancies\n");        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
   fprintf(ficresvij,"# Age");        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
   for(i=1; i<=nlstate;i++)        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
     for(j=1; j<=nlstate;j++)        /* Thus we compare delta(2h) with observed f1-f3 */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        /* or best gain on one ancient line 'del' with total  */
   fprintf(ficresvij,"\n");        /* gain f1-f2 = f1 - f2 - 'del' with del  */
         /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
   doldm=matrix(1,nlstate,1,nlstate);        t= t- del*SQR(fp-fptt);
          printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
   hstepm=1*YEARM; /* Every year of age */        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);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  #ifdef DEBUG
   agelim = AGESUP;        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
     if (stepm >= YEARM) hstepm=1;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        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);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        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);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  #endif
     gp=matrix(0,nhstepm,1,nlstate);        if (t < 0.0) { /* Then we use it for last direction */
     gm=matrix(0,nhstepm,1,nlstate);          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
           for (j=1;j<=n;j++) { 
     for(theta=1; theta <=npar; theta++){            xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
       for(i=1; i<=npar; i++){ /* Computes gradient */            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }
       }          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(j=1; j<= nlstate; j++){  #ifdef DEBUG
         for(h=0; h<=nhstepm; h++){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          for(j=1;j<=n;j++){
         }            printf(" %.12e",xit[j]);
       }            fprintf(ficlog," %.12e",xit[j]);
              }
       for(i=1; i<=npar; i++) /* Computes gradient */          printf("\n");
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          fprintf(ficlog,"\n");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    #endif
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } /* end of t negative */
       for(j=1; j<= nlstate; j++){      } /* end if (fptt < fp)  */
         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];  
         }  /**** Prevalence limit (stable or period prevalence)  ****************/
       }  
       for(j=1; j<= nlstate; j++)  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         for(h=0; h<=nhstepm; h++){  {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         }       matrix by transitions matrix until convergence is reached */
     } /* End theta */  
     int i, ii,j,k;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    double min, max, maxmin, maxmax,sumnew=0.;
     /* double **matprod2(); */ /* test */
     for(h=0; h<=nhstepm; h++)    double **out, cov[NCOVMAX+1], **pmij();
       for(j=1; j<=nlstate;j++)    double **newm;
         for(theta=1; theta <=npar; theta++)    double agefin, delaymax=50 ; /* Max number of years to converge */
           trgradg[h][j][theta]=gradg[h][theta][j];  
     for (ii=1;ii<=nlstate+ndeath;ii++)
     for(i=1;i<=nlstate;i++)      for (j=1;j<=nlstate+ndeath;j++){
       for(j=1;j<=nlstate;j++)        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         vareij[i][j][(int)age] =0.;      }
     for(h=0;h<=nhstepm;h++){  
       for(k=0;k<=nhstepm;k++){     cov[1]=1.;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);   
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         for(i=1;i<=nlstate;i++)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
           for(j=1;j<=nlstate;j++)      newm=savm;
             vareij[i][j][(int)age] += doldm[i][j];      /* Covariates have to be included here again */
       }      cov[2]=agefin;
     }      
     h=1;      for (k=1; k<=cptcovn;k++) {
     if (stepm >= YEARM) h=stepm/YEARM;        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     fprintf(ficresvij,"%.0f ",age );        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
     for(i=1; i<=nlstate;i++)      }
       for(j=1; j<=nlstate;j++){      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
       }      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
     fprintf(ficresvij,"\n");      
     free_matrix(gp,0,nhstepm,1,nlstate);      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     free_matrix(gm,0,nhstepm,1,nlstate);      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
   } /* End age */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
        
   free_vector(xp,1,npar);      savm=oldm;
   free_matrix(doldm,1,nlstate,1,npar);      oldm=newm;
   free_matrix(dnewm,1,nlstate,1,nlstate);      maxmax=0.;
       for(j=1;j<=nlstate;j++){
 }        min=1.;
         max=0.;
 /************ Variance of prevlim ******************/        for(i=1; i<=nlstate; i++) {
 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)          sumnew=0;
 {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   /* Variance of prevalence limit */          prlim[i][j]= newm[i][j]/(1-sumnew);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
   double **newm;          max=FMAX(max,prlim[i][j]);
   double **dnewm,**doldm;          min=FMIN(min,prlim[i][j]);
   int i, j, nhstepm, hstepm;        }
   int k, cptcode;        maxmin=max-min;
   double *xp;        maxmax=FMAX(maxmax,maxmin);
   double *gp, *gm;      }
   double **gradg, **trgradg;      if(maxmax < ftolpl){
   double age,agelim;        return prlim;
   int theta;      }
        }
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  }
   fprintf(ficresvpl,"# Age");  
   for(i=1; i<=nlstate;i++)  /*************** transition probabilities ***************/ 
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
   xp=vector(1,npar);    /* According to parameters values stored in x and the covariate's values stored in cov,
   dnewm=matrix(1,nlstate,1,npar);       computes the probability to be observed in state j being in state i by appying the
   doldm=matrix(1,nlstate,1,nlstate);       model to the ncovmodel covariates (including constant and age).
         lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
   hstepm=1*YEARM; /* Every year of age */       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */       ncth covariate in the global vector x is given by the formula:
   agelim = AGESUP;       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
     if (stepm >= YEARM) hstepm=1;       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */       Outputs ps[i][j] the probability to be observed in j being in j according to
     gradg=matrix(1,npar,1,nlstate);       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     gp=vector(1,nlstate);    */
     gm=vector(1,nlstate);    double s1, lnpijopii;
     /*double t34;*/
     for(theta=1; theta <=npar; theta++){    int i,j, nc, ii, jj;
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      for(i=1; i<= nlstate; i++){
       }        for(j=1; j<i;j++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       for(i=1;i<=nlstate;i++)            /*lnpijopii += param[i][j][nc]*cov[nc];*/
         gp[i] = prlim[i][i];            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
      /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       for(i=1; i<=npar; i++) /* Computes gradient */          }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       for(i=1;i<=nlstate;i++)        }
         gm[i] = prlim[i][i];        for(j=i+1; j<=nlstate+ndeath;j++){
           for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       for(i=1;i<=nlstate;i++)            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
     } /* End theta */  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
           }
     trgradg =matrix(1,nlstate,1,npar);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         }
     for(j=1; j<=nlstate;j++)      }
       for(theta=1; theta <=npar; theta++)      
         trgradg[j][theta]=gradg[theta][j];      for(i=1; i<= nlstate; i++){
         s1=0;
     for(i=1;i<=nlstate;i++)        for(j=1; j<i; j++){
       varpl[i][(int)age] =0.;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        }
     for(i=1;i<=nlstate;i++)        for(j=i+1; j<=nlstate+ndeath; j++){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          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); */
     fprintf(ficresvpl,"%.0f ",age );        }
     for(i=1; i<=nlstate;i++)        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        ps[i][i]=1./(s1+1.);
     fprintf(ficresvpl,"\n");        /* Computing other pijs */
     free_vector(gp,1,nlstate);        for(j=1; j<i; j++)
     free_vector(gm,1,nlstate);          ps[i][j]= exp(ps[i][j])*ps[i][i];
     free_matrix(gradg,1,npar,1,nlstate);        for(j=i+1; j<=nlstate+ndeath; j++)
     free_matrix(trgradg,1,nlstate,1,npar);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   } /* End age */        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       } /* end i */
   free_vector(xp,1,npar);      
   free_matrix(doldm,1,nlstate,1,npar);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   free_matrix(dnewm,1,nlstate,1,nlstate);        for(jj=1; jj<= nlstate+ndeath; jj++){
           ps[ii][jj]=0;
 }          ps[ii][ii]=1;
         }
       }
       
 /***********************************************/      
 /**************** Main Program *****************/      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
 /***********************************************/      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
       /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
 /*int main(int argc, char *argv[])*/      /*   } */
 int main()      /*   printf("\n "); */
 {      /* } */
       /* printf("\n ");printf("%lf ",cov[2]);*/
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      /*
   double agedeb, agefin,hf;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   double agemin=1.e20, agemax=-1.e20;        goto end;*/
       return ps;
   double fret;  }
   double **xi,tmp,delta;  
   /**************** Product of 2 matrices ******************/
   double dum; /* Dummy variable */  
   double ***p3mat;  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   int *indx;  {
   char line[MAXLINE], linepar[MAXLINE];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   char title[MAXLINE];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    /* in, b, out are matrice of pointers which should have been initialized 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];       before: only the contents of out is modified. The function returns
   char filerest[FILENAMELENGTH];       a pointer to pointers identical to out */
   char fileregp[FILENAMELENGTH];    int i, j, k;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    for(i=nrl; i<= nrh; i++)
   int firstobs=1, lastobs=10;      for(k=ncolol; k<=ncoloh; k++){
   int sdeb, sfin; /* Status at beginning and end */        out[i][k]=0.;
   int c,  h , cpt,l;        for(j=ncl; j<=nch; j++)
   int ju,jl, mi;          out[i][k] +=in[i][j]*b[j][k];
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    return out;
    }
   int hstepm, nhstepm;  
   double bage, fage, age, agelim, agebase;  
   double ftolpl=FTOL;  /************* Higher Matrix Product ***************/
   double **prlim;  
   double *severity;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   double ***param; /* Matrix of parameters */  {
   double  *p;    /* Computes the transition matrix starting at age 'age' over 
   double **matcov; /* Matrix of covariance */       'nhstepm*hstepm*stepm' months (i.e. until
   double ***delti3; /* Scale */       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   double *delti; /* Scale */       nhstepm*hstepm matrices. 
   double ***eij, ***vareij;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   double **varpl; /* Variances of prevalence limits by age */       (typically every 2 years instead of every month which is too big 
   double *epj, vepp;       for the memory).
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";       Model is determined by parameters x and covariates have to be 
   char *alph[]={"a","a","b","c","d","e"}, str[4];       included manually here. 
   
   char z[1]="c", occ;       */
 #include <sys/time.h>  
 #include <time.h>    int i, j, d, h, k;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    double **out, cov[NCOVMAX+1];
   /* long total_usecs;    double **newm;
   struct timeval start_time, end_time;  
      /* Hstepm could be zero and should return the unit matrix */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
   printf("\nIMACH, Version 0.64b");        po[i][j][0]=(i==j ? 1.0 : 0.0);
   printf("\nEnter the parameter file name: ");      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 #ifdef windows    for(h=1; h <=nhstepm; h++){
   scanf("%s",pathtot);      for(d=1; d <=hstepm; d++){
   getcwd(pathcd, size);        newm=savm;
   /*cygwin_split_path(pathtot,path,optionfile);        /* Covariates have to be included here again */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        cov[1]=1.;
   /* cutv(path,optionfile,pathtot,'\\');*/        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) 
 split(pathtot, path,optionfile);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   chdir(path);        for (k=1; k<=cptcovage;k++)
   replace(pathc,path);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 #endif        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
 #ifdef unix          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   scanf("%s",optionfile);  
 #endif  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 /*-------- arguments in the command line --------*/        /*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, 
   strcpy(fileres,"r");                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   strcat(fileres, optionfile);        savm=oldm;
         oldm=newm;
   /*---------arguments file --------*/      }
       for(i=1; i<=nlstate+ndeath; i++)
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        for(j=1;j<=nlstate+ndeath;j++) {
     printf("Problem with optionfile %s\n",optionfile);          po[i][j][h]=newm[i][j];
     goto end;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   }        }
       /*printf("h=%d ",h);*/
   strcpy(filereso,"o");    } /* end h */
   strcat(filereso,fileres);  /*     printf("\n H=%d \n",h); */
   if((ficparo=fopen(filereso,"w"))==NULL) {    return po;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  }
   }  
   #ifdef NLOPT
   /* Reads comments: lines beginning with '#' */    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
   while((c=getc(ficpar))=='#' && c!= EOF){    double fret;
     ungetc(c,ficpar);    double *xt;
     fgets(line, MAXLINE, ficpar);    int j;
     puts(line);    myfunc_data *d2 = (myfunc_data *) pd;
     fputs(line,ficparo);  /* xt = (p1-1); */
   }    xt=vector(1,n); 
   ungetc(c,ficpar);    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
   
   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);    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
   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);    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
   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);    printf("Function = %.12lf ",fret);
     for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
   covar=matrix(0,NCOVMAX,1,n);    printf("\n");
   cptcovn=0;   free_vector(xt,1,n);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    return fret;
   }
   ncovmodel=2+cptcovn;  #endif
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
    /*************** log-likelihood *************/
   /* Read guess parameters */  double func( double *x)
   /* Reads comments: lines beginning with '#' */  {
   while((c=getc(ficpar))=='#' && c!= EOF){    int i, ii, j, k, mi, d, kk;
     ungetc(c,ficpar);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     fgets(line, MAXLINE, ficpar);    double **out;
     puts(line);    double sw; /* Sum of weights */
     fputs(line,ficparo);    double lli; /* Individual log likelihood */
   }    int s1, s2;
   ungetc(c,ficpar);    double bbh, survp;
      long ipmx;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    /*extern weight */
     for(i=1; i <=nlstate; i++)    /* We are differentiating ll according to initial status */
     for(j=1; j <=nlstate+ndeath-1; j++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       fscanf(ficpar,"%1d%1d",&i1,&j1);    /*for(i=1;i<imx;i++) 
       fprintf(ficparo,"%1d%1d",i1,j1);      printf(" %d\n",s[4][i]);
       printf("%1d%1d",i,j);    */
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);    ++countcallfunc;
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);    cov[1]=1.;
       }  
       fscanf(ficpar,"\n");    for(k=1; k<=nlstate; k++) ll[k]=0.;
       printf("\n");  
       fprintf(ficparo,"\n");    if(mle==1){
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          /* Computes the values of the ncovmodel covariates of the model
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;           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
   p=param[1][1];           to be observed in j being in i according to the model.
           */
   /* Reads comments: lines beginning with '#' */        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
   while((c=getc(ficpar))=='#' && c!= EOF){          cov[2+k]=covar[Tvar[k]][i];
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
     puts(line);           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
     fputs(line,ficparo);           has been calculated etc */
   }        for(mi=1; mi<= wav[i]-1; mi++){
   ungetc(c,ficpar);          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(i=1; i <=nlstate; i++){            }
     for(j=1; j <=nlstate+ndeath-1; j++){          for(d=0; d<dh[mi][i]; d++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);            newm=savm;
       printf("%1d%1d",i,j);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       fprintf(ficparo,"%1d%1d",i1,j1);            for (kk=1; kk<=cptcovage;kk++) {
       for(k=1; k<=ncovmodel;k++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
         fscanf(ficpar,"%le",&delti3[i][j][k]);            }
         printf(" %le",delti3[i][j][k]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         fprintf(ficparo," %le",delti3[i][j][k]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
       fscanf(ficpar,"\n");            oldm=newm;
       printf("\n");          } /* end mult */
       fprintf(ficparo,"\n");        
     }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   }          /* But now since version 0.9 we anticipate for bias at large stepm.
   delti=delti3[1][1];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
             * (in months) between two waves is not a multiple of stepm, we rounded to 
   /* Reads comments: lines beginning with '#' */           * the nearest (and in case of equal distance, to the lowest) interval but now
   while((c=getc(ficpar))=='#' && c!= EOF){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     ungetc(c,ficpar);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
     fgets(line, MAXLINE, ficpar);           * probability in order to take into account the bias as a fraction of the way
     puts(line);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     fputs(line,ficparo);           * -stepm/2 to stepm/2 .
   }           * For stepm=1 the results are the same as for previous versions of Imach.
   ungetc(c,ficpar);           * For stepm > 1 the results are less biased than in previous versions. 
             */
   matcov=matrix(1,npar,1,npar);          s1=s[mw[mi][i]][i];
   for(i=1; i <=npar; i++){          s2=s[mw[mi+1][i]][i];
     fscanf(ficpar,"%s",&str);          bbh=(double)bh[mi][i]/(double)stepm; 
     printf("%s",str);          /* bias bh is positive if real duration
     fprintf(ficparo,"%s",str);           * is higher than the multiple of stepm and negative otherwise.
     for(j=1; j <=i; j++){           */
       fscanf(ficpar," %le",&matcov[i][j]);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       printf(" %.5le",matcov[i][j]);          if( s2 > nlstate){ 
       fprintf(ficparo," %.5le",matcov[i][j]);            /* i.e. if s2 is a death state and if the date of death is known 
     }               then the contribution to the likelihood is the probability to 
     fscanf(ficpar,"\n");               die between last step unit time and current  step unit time, 
     printf("\n");               which is also equal to probability to die before dh 
     fprintf(ficparo,"\n");               minus probability to die before dh-stepm . 
   }               In version up to 0.92 likelihood was computed
   for(i=1; i <=npar; i++)          as if date of death was unknown. Death was treated as any other
     for(j=i+1;j<=npar;j++)          health state: the date of the interview describes the actual state
       matcov[i][j]=matcov[j][i];          and not the date of a change in health state. The former idea was
              to consider that at each interview the state was recorded
   printf("\n");          (healthy, disable or death) and IMaCh was corrected; but when we
           introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
     /*-------- data file ----------*/          contribution is smaller and very dependent of the step unit
     if((ficres =fopen(fileres,"w"))==NULL) {          stepm. It is no more the probability to die between last interview
       printf("Problem with resultfile: %s\n", fileres);goto end;          and month of death but the probability to survive from last
     }          interview up to one month before death multiplied by the
     fprintf(ficres,"#%s\n",version);          probability to die within a month. Thanks to Chris
              Jackson for correcting this bug.  Former versions increased
     if((fic=fopen(datafile,"r"))==NULL)    {          mortality artificially. The bad side is that we add another loop
       printf("Problem with datafile: %s\n", datafile);goto end;          which slows down the processing. The difference can be up to 10%
     }          lower mortality.
             */
     n= lastobs;            lli=log(out[s1][s2] - savm[s1][s2]);
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);  
     num=ivector(1,n);          } else if  (s2==-2) {
     moisnais=vector(1,n);            for (j=1,survp=0. ; j<=nlstate; j++) 
     annais=vector(1,n);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     moisdc=vector(1,n);            /*survp += out[s1][j]; */
     andc=vector(1,n);            lli= log(survp);
     agedc=vector(1,n);          }
     cod=ivector(1,n);          
     weight=vector(1,n);          else if  (s2==-4) { 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            for (j=3,survp=0. ; j<=nlstate; j++)  
     mint=matrix(1,maxwav,1,n);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     anint=matrix(1,maxwav,1,n);            lli= log(survp); 
     s=imatrix(1,maxwav+1,1,n);          } 
     adl=imatrix(1,maxwav+1,1,n);      
     tab=ivector(1,NCOVMAX);          else if  (s2==-5) { 
     ncodemax=ivector(1,8);            for (j=1,survp=0. ; j<=2; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     i=1;            lli= log(survp); 
     while (fgets(line, MAXLINE, fic) != NULL)    {          } 
       if ((i >= firstobs) && (i <=lastobs)) {          
                  else{
         for (j=maxwav;j>=1;j--){            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            /*  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 */
           strcpy(line,stra);          } 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          /*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); */
                  ipmx +=1;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          sw += weight[i];
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      } /* end of individual */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for (j=ncov;j>=1;j--){        for(mi=1; mi<= wav[i]-1; mi++){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for (ii=1;ii<=nlstate+ndeath;ii++)
         }            for (j=1;j<=nlstate+ndeath;j++){
         num[i]=atol(stra);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                      savm[ii][j]=(ii==j ? 1.0 : 0.0);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            }
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
         i=i+1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     /* printf("ii=%d", ij);            }
        scanf("%d",i);*/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   imx=i-1; /* Number of individuals */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   /* for (i=1; i<=imx; i++){            oldm=newm;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          } /* end mult */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
   for (i=1; i<=imx; i++) 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]));*/          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   /* Calculation of the number of parameter from char model*/          ipmx +=1;
   Tvar=ivector(1,15);          sw += weight[i];
   Tprod=ivector(1,15);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   Tvaraff=ivector(1,15);        } /* end of wave */
   Tvard=imatrix(1,15,1,2);      } /* end of individual */
   Tage=ivector(1,15);          }  else if(mle==3){  /* exponential inter-extrapolation */
          for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   if (strlen(model) >1){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     j=0, j1=0, k1=1, k2=1;        for(mi=1; mi<= wav[i]-1; mi++){
     j=nbocc(model,'+');          for (ii=1;ii<=nlstate+ndeath;ii++)
     j1=nbocc(model,'*');            for (j=1;j<=nlstate+ndeath;j++){
     cptcovn=j+1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     cptcovprod=j1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                }
              for(d=0; d<dh[mi][i]; d++){
     strcpy(modelsav,model);            newm=savm;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       printf("Error. Non available option model=%s ",model);            for (kk=1; kk<=cptcovage;kk++) {
       goto end;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }            }
                out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(i=(j+1); i>=1;i--){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       cutv(stra,strb,modelsav,'+');            savm=oldm;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);            oldm=newm;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          } /* end mult */
       /*scanf("%d",i);*/        
       if (strchr(strb,'*')) {          s1=s[mw[mi][i]][i];
         cutv(strd,strc,strb,'*');          s2=s[mw[mi+1][i]][i];
         if (strcmp(strc,"age")==0) {          bbh=(double)bh[mi][i]/(double)stepm; 
           cptcovprod--;          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 */
           cutv(strb,stre,strd,'V');          ipmx +=1;
           Tvar[i]=atoi(stre);          sw += weight[i];
           cptcovage++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             Tage[cptcovage]=i;        } /* end of wave */
             /*printf("stre=%s ", stre);*/      } /* end of individual */
         }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         else if (strcmp(strd,"age")==0) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           cptcovprod--;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           cutv(strb,stre,strc,'V');        for(mi=1; mi<= wav[i]-1; mi++){
           Tvar[i]=atoi(stre);          for (ii=1;ii<=nlstate+ndeath;ii++)
           cptcovage++;            for (j=1;j<=nlstate+ndeath;j++){
           Tage[cptcovage]=i;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         else {            }
           cutv(strb,stre,strc,'V');          for(d=0; d<dh[mi][i]; d++){
           Tvar[i]=ncov+k1;            newm=savm;
           cutv(strb,strc,strd,'V');            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           Tprod[k1]=i;            for (kk=1; kk<=cptcovage;kk++) {
           Tvard[k1][1]=atoi(strc);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           Tvard[k1][2]=atoi(stre);            }
           Tvar[cptcovn+k2]=Tvard[k1][1];          
           Tvar[cptcovn+k2+1]=Tvard[k1][2];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           for (k=1; k<=lastobs;k++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];            savm=oldm;
           k1++;            oldm=newm;
           k2=k2+2;          } /* end mult */
         }        
       }          s1=s[mw[mi][i]][i];
       else {          s2=s[mw[mi+1][i]][i];
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          if( s2 > nlstate){ 
        /*  scanf("%d",i);*/            lli=log(out[s1][s2] - savm[s1][s2]);
       cutv(strd,strc,strb,'V');          }else{
       Tvar[i]=atoi(strc);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       }          }
       strcpy(modelsav,stra);            ipmx +=1;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          sw += weight[i];
         scanf("%d",i);*/          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]); */
 }        } /* end of wave */
        } /* end of individual */
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   printf("cptcovprod=%d ", cptcovprod);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   scanf("%d ",i);*/        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fclose(fic);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
     /*  if(mle==1){*/            for (j=1;j<=nlstate+ndeath;j++){
     if (weightopt != 1) { /* Maximisation without weights*/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1;i<=n;i++) weight[i]=1.0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
     /*-calculation of age at interview from date of interview and age at death -*/          for(d=0; d<dh[mi][i]; d++){
     agev=matrix(1,maxwav,1,imx);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
    for (i=1; i<=imx; i++)            for (kk=1; kk<=cptcovage;kk++) {
      for(m=2; (m<= maxwav); m++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){            }
          anint[m][i]=9999;          
          s[m][i]=-1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
        }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
     for (i=1; i<=imx; i++)  {            oldm=newm;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          } /* end mult */
       for(m=1; (m<= maxwav); m++){        
         if(s[m][i] >0){          s1=s[mw[mi][i]][i];
           if (s[m][i] == nlstate+1) {          s2=s[mw[mi+1][i]][i];
             if(agedc[i]>0)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
               if(moisdc[i]!=99 && andc[i]!=9999)          ipmx +=1;
               agev[m][i]=agedc[i];          sw += weight[i];
             else {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               if (andc[i]!=9999){          /*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("Warning negative age at death: %d line:%d\n",num[i],i);        } /* end of wave */
               agev[m][i]=-1;      } /* end of individual */
               }    } /* End of if */
             }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           else if(s[m][i] !=9){ /* Should no more exist */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    return -l;
             if(mint[m][i]==99 || anint[m][i]==9999)  }
               agev[m][i]=1;  
             else if(agev[m][i] <agemin){  /*************** log-likelihood *************/
               agemin=agev[m][i];  double funcone( double *x)
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  {
             }    /* Same as likeli but slower because of a lot of printf and if */
             else if(agev[m][i] >agemax){    int i, ii, j, k, mi, d, kk;
               agemax=agev[m][i];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    double **out;
             }    double lli; /* Individual log likelihood */
             /*agev[m][i]=anint[m][i]-annais[i];*/    double llt;
             /*   agev[m][i] = age[i]+2*m;*/    int s1, s2;
           }    double bbh, survp;
           else { /* =9 */    /*extern weight */
             agev[m][i]=1;    /* We are differentiating ll according to initial status */
             s[m][i]=-1;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           }    /*for(i=1;i<imx;i++) 
         }      printf(" %d\n",s[4][i]);
         else /*= 0 Unknown */    */
           agev[m][i]=1;    cov[1]=1.;
       }  
        for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
     for (i=1; i<=imx; i++)  {    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(m=1; (m<= maxwav); m++){      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if (s[m][i] > (nlstate+ndeath)) {      for(mi=1; mi<= wav[i]-1; mi++){
           printf("Error: Wrong value in nlstate or ndeath\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
           goto end;          for (j=1;j<=nlstate+ndeath;j++){
         }            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }          }
         for(d=0; d<dh[mi][i]; d++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     free_vector(severity,1,maxwav);          for (kk=1; kk<=cptcovage;kk++) {
     free_imatrix(outcome,1,maxwav+1,1,n);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     free_vector(moisnais,1,n);          }
     free_vector(annais,1,n);          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     free_matrix(mint,1,maxwav,1,n);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_matrix(anint,1,maxwav,1,n);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_vector(moisdc,1,n);          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
     free_vector(andc,1,n);          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
           savm=oldm;
              oldm=newm;
     wav=ivector(1,imx);        } /* end mult */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
     /* Concatenates waves */        bbh=(double)bh[mi][i]/(double)stepm; 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
          */
       Tcode=ivector(1,100);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          lli=log(out[s1][s2] - savm[s1][s2]);
       ncodemax[1]=1;        } else if  (s2==-2) {
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          for (j=1,survp=0. ; j<=nlstate; j++) 
                  survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
    codtab=imatrix(1,100,1,10);          lli= log(survp);
    h=0;        }else if (mle==1){
    m=pow(2,cptcoveff);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
          } else if(mle==2){
    for(k=1;k<=cptcoveff; k++){          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
      for(i=1; i <=(m/pow(2,k));i++){        } else if(mle==3){  /* exponential inter-extrapolation */
        for(j=1; j <= ncodemax[k]; j++){          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
            h++;          lli=log(out[s1][s2]); /* Original formula */
            if (h>m) h=1;codtab[h][k]=j;        } else{  /* mle=0 back to 1 */
          }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
        }          /*lli=log(out[s1][s2]); */ /* Original formula */
      }        } /* End of if */
    }        ipmx +=1;
         sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
    /*for(i=1; i <=m ;i++){        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
      for(k=1; k <=cptcovn; k++){        if(globpr){
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
      }   %11.6f %11.6f %11.6f ", \
      printf("\n");                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
    }                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
    scanf("%d",i);*/          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                llt +=ll[k]*gipmx/gsw;
    /* Calculates basic frequencies. Computes observed prevalence at single age            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
        and prints on file fileres'p'. */          }
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);          fprintf(ficresilk," %10.6f\n", -llt);
         }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      } /* end of wave */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    } /* end of individual */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    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 */
     /* For Powell, parameters are in a vector p[] starting at p[1]      gipmx=ipmx;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      gsw=sw;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    }
     return -l;
     if(mle==1){  }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }  
      /*************** function likelione ***********/
     /*--------- results files --------------*/  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     fprintf(ficres,"\ntitle=%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);  {
        /* This routine should help understanding what is done with 
    jk=1;       the selection of individuals/waves and
    fprintf(ficres,"# Parameters\n");       to check the exact contribution to the likelihood.
    printf("# Parameters\n");       Plotting could be done.
    for(i=1,jk=1; i <=nlstate; i++){     */
      for(k=1; k <=(nlstate+ndeath); k++){    int k;
        if (k != i)  
          {    if(*globpri !=0){ /* Just counts and sums, no printings */
            printf("%d%d ",i,k);      strcpy(fileresilk,"ilk"); 
            fprintf(ficres,"%1d%1d ",i,k);      strcat(fileresilk,fileres);
            for(j=1; j <=ncovmodel; j++){      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
              printf("%f ",p[jk]);        printf("Problem with resultfile: %s\n", fileresilk);
              fprintf(ficres,"%f ",p[jk]);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
              jk++;      }
            }      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
            printf("\n");      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
            fprintf(ficres,"\n");      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
          }      for(k=1; k<=nlstate; k++) 
      }        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
    }      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
  if(mle==1){    }
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */    *fretone=(*funcone)(p);
     hesscov(matcov, p, npar, delti, ftolhess, func);    if(*globpri !=0){
  }      fclose(ficresilk);
     fprintf(ficres,"# Scales\n");      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     printf("# Scales\n");      fflush(fichtm); 
      for(i=1,jk=1; i <=nlstate; i++){    } 
       for(j=1; j <=nlstate+ndeath; j++){    return;
         if (j!=i) {  }
           fprintf(ficres,"%1d%1d",i,j);  
           printf("%1d%1d",i,j);  
           for(k=1; k<=ncovmodel;k++){  /*********** Maximum Likelihood Estimation ***************/
             printf(" %.5e",delti[jk]);  
             fprintf(ficres," %.5e",delti[jk]);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
             jk++;  {
           }    int i,j, iter=0;
           printf("\n");    double **xi;
           fprintf(ficres,"\n");    double fret;
         }    double fretone; /* Only one call to likelihood */
       }    /*  char filerespow[FILENAMELENGTH];*/
       }  
      #ifdef NLOPT
     k=1;    int creturn;
     fprintf(ficres,"# Covariance\n");    nlopt_opt opt;
     printf("# Covariance\n");    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     for(i=1;i<=npar;i++){    double *lb;
       /*  if (k>nlstate) k=1;    double minf; /* the minimum objective value, upon return */
       i1=(i-1)/(ncovmodel*nlstate)+1;    double * p1; /* Shifted parameters from 0 instead of 1 */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    myfunc_data dinst, *d = &dinst;
       printf("%s%d%d",alph[k],i1,tab[i]);*/  #endif
       fprintf(ficres,"%3d",i);  
       printf("%3d",i);  
       for(j=1; j<=i;j++){    xi=matrix(1,npar,1,npar);
         fprintf(ficres," %.5e",matcov[i][j]);    for (i=1;i<=npar;i++)
         printf(" %.5e",matcov[i][j]);      for (j=1;j<=npar;j++)
       }        xi[i][j]=(i==j ? 1.0 : 0.0);
       fprintf(ficres,"\n");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       printf("\n");    strcpy(filerespow,"pow"); 
       k++;    strcat(filerespow,fileres);
     }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", filerespow);
     while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       ungetc(c,ficpar);    }
       fgets(line, MAXLINE, ficpar);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       puts(line);    for (i=1;i<=nlstate;i++)
       fputs(line,ficparo);      for(j=1;j<=nlstate+ndeath;j++)
     }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     ungetc(c,ficpar);    fprintf(ficrespow,"\n");
    #ifdef POWELL
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    powell(p,xi,npar,ftol,&iter,&fret,func);
      #endif
     if (fage <= 2) {  
       bage = agemin;  #ifdef NLOPT
       fage = agemax;  #ifdef NEWUOA
     }    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   #else
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  #endif
     lb=vector(0,npar-1);
        for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
 /*------------ gnuplot -------------*/    nlopt_set_lower_bounds(opt, lb);
 chdir(pathcd);    nlopt_set_initial_step1(opt, 0.1);
   if((ficgp=fopen("graph.plt","w"))==NULL) {    
     printf("Problem with file graph.gp");goto end;    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   }    d->function = func;
 #ifdef windows    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
   fprintf(ficgp,"cd \"%s\" \n",pathc);    nlopt_set_min_objective(opt, myfunc, d);
 #endif    nlopt_set_xtol_rel(opt, ftol);
 m=pow(2,cptcoveff);    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
        printf("nlopt failed! %d\n",creturn); 
  /* 1eme*/    }
   for (cpt=1; cpt<= nlstate ; cpt ++) {    else {
    for (k1=1; k1<= m ; k1 ++) {      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
       printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
 #ifdef windows      iter=1; /* not equal */
     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);    }
 #endif    nlopt_destroy(opt);
 #ifdef unix  #endif
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    free_matrix(xi,1,npar,1,npar);
 #endif    fclose(ficrespow);
     printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
 for (i=1; i<= nlstate ; i ++) {    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }  }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  
     for (i=1; i<= nlstate ; i ++) {  /**** Computes Hessian and covariance matrix ***/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   else fprintf(ficgp," \%%*lf (\%%*lf)");  {
 }    double  **a,**y,*x,pd;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    double **hess;
      for (i=1; i<= nlstate ; i ++) {    int i, j;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    int *indx;
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
 #ifdef unix    void lubksb(double **a, int npar, int *indx, double b[]) ;
 fprintf(ficgp,"\nset ter gif small size 400,300");    void ludcmp(double **a, int npar, int *indx, double *d) ;
 #endif    double gompertz(double p[]);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    hess=matrix(1,npar,1,npar);
    }  
   }    printf("\nCalculation of the hessian matrix. Wait...\n");
   /*2 eme*/    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
   for (k1=1; k1<= m ; k1 ++) {      printf("%d",i);fflush(stdout);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);      fprintf(ficlog,"%d",i);fflush(ficlog);
         
     for (i=1; i<= nlstate+1 ; i ++) {       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       k=2*i;      
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      /*  printf(" %f ",p[i]);
       for (j=1; j<= nlstate+1 ; j ++) {          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    
 }      for (i=1;i<=npar;i++) {
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      for (j=1;j<=npar;j++)  {
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        if (j>i) { 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          printf(".%d%d",i,j);fflush(stdout);
       for (j=1; j<= nlstate+1 ; j ++) {          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          hess[i][j]=hessij(p,delti,i,j,func,npar);
         else fprintf(ficgp," \%%*lf (\%%*lf)");          
 }            hess[j][i]=hess[i][j];    
       fprintf(ficgp,"\" t\"\" w l 0,");          /*printf(" %lf ",hess[i][j]);*/
      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)");    printf("\n");
 }      fprintf(ficlog,"\n");
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  
       else fprintf(ficgp,"\" t\"\" w l 0,");    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    
   }    a=matrix(1,npar,1,npar);
      y=matrix(1,npar,1,npar);
   /*3eme*/    x=vector(1,npar);
     indx=ivector(1,npar);
   for (k1=1; k1<= m ; k1 ++) {    for (i=1;i<=npar;i++)
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       k=2+nlstate*(cpt-1);    ludcmp(a,npar,indx,&pd);
       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 (j=1;j<=npar;j++) {
         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);      for (i=1;i<=npar;i++) x[i]=0;
       }      x[j]=1;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      lubksb(a,npar,indx,x);
     }      for (i=1;i<=npar;i++){ 
   }        matcov[i][j]=x[i];
        }
   /* CV preval stat */    }
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {    printf("\n#Hessian matrix#\n");
       k=3;    fprintf(ficlog,"\n#Hessian matrix#\n");
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    for (i=1;i<=npar;i++) { 
       for (i=1; i< nlstate ; i ++)      for (j=1;j<=npar;j++) { 
         fprintf(ficgp,"+$%d",k+i+1);        printf("%.3e ",hess[i][j]);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        fprintf(ficlog,"%.3e ",hess[i][j]);
            }
       l=3+(nlstate+ndeath)*cpt;      printf("\n");
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      fprintf(ficlog,"\n");
       for (i=1; i< nlstate ; i ++) {    }
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);    /* Recompute Inverse */
       }    for (i=1;i<=npar;i++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    ludcmp(a,npar,indx,&pd);
     }  
   }    /*  printf("\n#Hessian matrix recomputed#\n");
   
   /* proba elementaires */    for (j=1;j<=npar;j++) {
    for(i=1,jk=1; i <=nlstate; i++){      for (i=1;i<=npar;i++) x[i]=0;
     for(k=1; k <=(nlstate+ndeath); k++){      x[j]=1;
       if (k != i) {      lubksb(a,npar,indx,x);
         for(j=1; j <=ncovmodel; j++){      for (i=1;i<=npar;i++){ 
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/        y[i][j]=x[i];
           /*fprintf(ficgp,"%s",alph[1]);*/        printf("%.3e ",y[i][j]);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        fprintf(ficlog,"%.3e ",y[i][j]);
           jk++;      }
           fprintf(ficgp,"\n");      printf("\n");
         }      fprintf(ficlog,"\n");
       }    }
     }    */
     }  
     free_matrix(a,1,npar,1,npar);
   for(jk=1; jk <=m; jk++) {    free_matrix(y,1,npar,1,npar);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    free_vector(x,1,npar);
    i=1;    free_ivector(indx,1,npar);
    for(k2=1; k2<=nlstate; k2++) {    free_matrix(hess,1,npar,1,npar);
      k3=i;  
      for(k=1; k<=(nlstate+ndeath); k++) {  
        if (k != k2){  }
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  
 ij=1;  /*************** hessian matrix ****************/
         for(j=3; j <=ncovmodel; j++) {  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  {
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    int i;
             ij++;    int l=1, lmax=20;
           }    double k1,k2;
           else    double p2[MAXPARM+1]; /* identical to x */
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    double res;
         }    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           fprintf(ficgp,")/(1");    double fx;
            int k=0,kmax=10;
         for(k1=1; k1 <=nlstate; k1++){      double l1;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  
 ij=1;    fx=func(x);
           for(j=3; j <=ncovmodel; j++){    for (i=1;i<=npar;i++) p2[i]=x[i];
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      l1=pow(10,l);
             ij++;      delts=delt;
           }      for(k=1 ; k <kmax; k=k+1){
           else        delt = delta*(l1*k);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        p2[theta]=x[theta] +delt;
           }        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
           fprintf(ficgp,")");        p2[theta]=x[theta]-delt;
         }        k2=func(p2)-fx;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        /*res= (k1-2.0*fx+k2)/delt/delt; */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         i=i+ncovmodel;        
        }  #ifdef DEBUGHESS
      }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
    }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  #endif
   }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
            if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   fclose(ficgp);          k=kmax;
            }
 chdir(path);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     free_matrix(agev,1,maxwav,1,imx);          k=kmax; l=lmax*10;
     free_ivector(wav,1,imx);        }
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          delts=delt;
            }
     free_imatrix(s,1,maxwav+1,1,n);      }
        }
        delti[theta]=delts;
     free_ivector(num,1,n);    return res; 
     free_vector(agedc,1,n);    
     free_vector(weight,1,n);  }
     /*free_matrix(covar,1,NCOVMAX,1,n);*/  
     fclose(ficparo);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     fclose(ficres);  {
     /*  }*/    int i;
        int l=1, lmax=20;
    /*________fin mle=1_________*/    double k1,k2,k3,k4,res,fx;
        double p2[MAXPARM+1];
     int k;
    
     /* No more information from the sample is required now */    fx=func(x);
   /* Reads comments: lines beginning with '#' */    for (k=1; k<=2; k++) {
   while((c=getc(ficpar))=='#' && c!= EOF){      for (i=1;i<=npar;i++) p2[i]=x[i];
     ungetc(c,ficpar);      p2[thetai]=x[thetai]+delti[thetai]/k;
     fgets(line, MAXLINE, ficpar);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     puts(line);      k1=func(p2)-fx;
     fputs(line,ficparo);    
   }      p2[thetai]=x[thetai]+delti[thetai]/k;
   ungetc(c,ficpar);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k2=func(p2)-fx;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);      p2[thetai]=x[thetai]-delti[thetai]/k;
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 /*--------- index.htm --------*/      k3=func(p2)-fx;
     
   strcpy(optionfilehtm,optionfile);      p2[thetai]=x[thetai]-delti[thetai]/k;
   strcat(optionfilehtm,".htm");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      k4=func(p2)-fx;
     printf("Problem with %s \n",optionfilehtm);goto end;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   }  #ifdef DEBUG
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">      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);
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>  #endif
 Total number of observations=%d <br>    }
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    return res;
 <hr  size=\"2\" color=\"#EC5E5E\">  }
 <li>Outputs files<br><br>\n  
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  /************** Inverse of matrix **************/
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  void ludcmp(double **a, int n, int *indx, double *d) 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>  { 
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    int i,imax,j,k; 
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    double big,dum,sum,temp; 
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    double *vv; 
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>   
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    vv=vector(1,n); 
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%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);    *d=1.0; 
     for (i=1;i<=n;i++) { 
  fprintf(fichtm," <li>Graphs</li><p>");      big=0.0; 
       for (j=1;j<=n;j++) 
  m=cptcoveff;        if ((temp=fabs(a[i][j])) > big) big=temp; 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
  j1=0;    } 
  for(k1=1; k1<=m;k1++){    for (j=1;j<=n;j++) { 
    for(i1=1; i1<=ncodemax[k1];i1++){      for (i=1;i<j;i++) { 
        j1++;        sum=a[i][j]; 
        if (cptcovn > 0) {        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        a[i][j]=sum; 
          for (cpt=1; cpt<=cptcoveff;cpt++)      } 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);      big=0.0; 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      for (i=j;i<=n;i++) { 
        }        sum=a[i][j]; 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        for (k=1;k<j;k++) 
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              sum -= a[i][k]*a[k][j]; 
        for(cpt=1; cpt<nlstate;cpt++){        a[i][j]=sum; 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        if ( (dum=vv[i]*fabs(sum)) >= big) { 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          big=dum; 
        }          imax=i; 
     for(cpt=1; cpt<=nlstate;cpt++) {        } 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      } 
 interval) in state (%d): v%s%d%d.gif <br>      if (j != imax) { 
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          for (k=1;k<=n;k++) { 
      }          dum=a[imax][k]; 
      for(cpt=1; cpt<=nlstate;cpt++) {          a[imax][k]=a[j][k]; 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          a[j][k]=dum; 
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        } 
      }        *d = -(*d); 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        vv[imax]=vv[j]; 
 health expectancies in states (1) and (2): e%s%d.gif<br>      } 
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      indx[j]=imax; 
 fprintf(fichtm,"\n</body>");      if (a[j][j] == 0.0) a[j][j]=TINY; 
    }      if (j != n) { 
  }        dum=1.0/(a[j][j]); 
 fclose(fichtm);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
   /*--------------- Prevalence limit --------------*/    } 
      free_vector(vv,1,n);  /* Doesn't work */
   strcpy(filerespl,"pl");  ;
   strcat(filerespl,fileres);  } 
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  void lubksb(double **a, int n, int *indx, double b[]) 
   }  { 
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    int i,ii=0,ip,j; 
   fprintf(ficrespl,"#Prevalence limit\n");    double sum; 
   fprintf(ficrespl,"#Age ");   
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    for (i=1;i<=n;i++) { 
   fprintf(ficrespl,"\n");      ip=indx[i]; 
        sum=b[ip]; 
   prlim=matrix(1,nlstate,1,nlstate);      b[ip]=b[i]; 
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      if (ii) 
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      else if (sum) ii=i; 
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      b[i]=sum; 
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    } 
   k=0;    for (i=n;i>=1;i--) { 
   agebase=agemin;      sum=b[i]; 
   agelim=agemax;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   ftolpl=1.e-10;      b[i]=sum/a[i][i]; 
   i1=cptcoveff;    } 
   if (cptcovn < 1){i1=1;}  } 
   
   for(cptcov=1;cptcov<=i1;cptcov++){  void pstamp(FILE *fichier)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  {
         k=k+1;    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  }
         fprintf(ficrespl,"\n#******");  
         for(j=1;j<=cptcoveff;j++)  /************ Frequencies ********************/
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
         fprintf(ficrespl,"******\n");  {  /* Some frequencies */
            
         for (age=agebase; age<=agelim; age++){    int i, m, jk, j1, bool, z1,j;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    int first;
           fprintf(ficrespl,"%.0f",age );    double ***freq; /* Frequencies */
           for(i=1; i<=nlstate;i++)    double *pp, **prop;
           fprintf(ficrespl," %.5f", prlim[i][i]);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
           fprintf(ficrespl,"\n");    char fileresp[FILENAMELENGTH];
         }    
       }    pp=vector(1,nlstate);
     }    prop=matrix(1,nlstate,iagemin,iagemax+3);
   fclose(ficrespl);    strcpy(fileresp,"p");
   /*------------- h Pij x at various ages ------------*/    strcat(fileresp,fileres);
      if((ficresp=fopen(fileresp,"w"))==NULL) {
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      printf("Problem with prevalence resultfile: %s\n", fileresp);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      exit(0);
   }    }
   printf("Computing pij: result on file '%s' \n", filerespij);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
      j1=0;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    
   if (stepm<=24) stepsize=2;    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
   agelim=AGESUP;  
   hstepm=stepsize*YEARM; /* Every year of age */    first=1;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  
      /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
   k=0;    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
   for(cptcov=1;cptcov<=i1;cptcov++){    /*    j1++;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  */
       k=k+1;    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
         fprintf(ficrespij,"\n#****** ");        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         for(j=1;j<=cptcoveff;j++)          scanf("%d", i);*/
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for (i=-5; i<=nlstate+ndeath; i++)  
         fprintf(ficrespij,"******\n");          for (jk=-5; jk<=nlstate+ndeath; jk++)  
                    for(m=iagemin; m <= iagemax+3; m++)
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */              freq[i][jk][m]=0;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        for (i=1; i<=nlstate; i++)  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(m=iagemin; m <= iagemax+3; m++)
           oldm=oldms;savm=savms;            prop[i][m]=0;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          
           fprintf(ficrespij,"# Age");        dateintsum=0;
           for(i=1; i<=nlstate;i++)        k2cpt=0;
             for(j=1; j<=nlstate+ndeath;j++)        for (i=1; i<=imx; i++) {
               fprintf(ficrespij," %1d-%1d",i,j);          bool=1;
           fprintf(ficrespij,"\n");          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
           for (h=0; h<=nhstepm; h++){            for (z1=1; z1<=cptcoveff; z1++)       
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
             for(i=1; i<=nlstate;i++)                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
               for(j=1; j<=nlstate+ndeath;j++)                bool=0;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                /* 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", 
             fprintf(ficrespij,"\n");                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
           }                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
           fprintf(ficrespij,"\n");              } 
         }          }
     }   
   }          if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
   fclose(ficrespij);              k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   /*---------- Health expectancies and variances ------------*/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
   strcpy(filerest,"t");                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   strcat(filerest,fileres);                if (m<lastpass) {
   if((ficrest=fopen(filerest,"w"))==NULL) {                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   }                }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
   strcpy(filerese,"e");                  k2cpt++;
   strcat(filerese,fileres);                }
   if((ficreseij=fopen(filerese,"w"))==NULL) {                /*}*/
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);            }
   }          }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        } /* end i */
          
  strcpy(fileresv,"v");        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   strcat(fileresv,fileres);        pstamp(ficresp);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        if  (cptcovn>0) {
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          fprintf(ficresp, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          fprintf(ficresp, "**********\n#");
           fprintf(ficlog, "\n#********** Variable "); 
   k=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficlog, "**********\n#");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }
       k=k+1;        for(i=1; i<=nlstate;i++) 
       fprintf(ficrest,"\n#****** ");          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       for(j=1;j<=cptcoveff;j++)        fprintf(ficresp, "\n");
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        
       fprintf(ficrest,"******\n");        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
       fprintf(ficreseij,"\n#****** ");            fprintf(ficlog,"Total");
       for(j=1;j<=cptcoveff;j++)          }else{
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);            if(first==1){
       fprintf(ficreseij,"******\n");              first=0;
               printf("See log file for details...\n");
       fprintf(ficresvij,"\n#****** ");            }
       for(j=1;j<=cptcoveff;j++)            fprintf(ficlog,"Age %d", i);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          }
       fprintf(ficresvij,"******\n");          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);              pp[jk] += freq[jk][m][i]; 
       oldm=oldms;savm=savms;          }
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);            for(jk=1; jk <=nlstate ; jk++){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            for(m=-1, pos=0; m <=0 ; m++)
       oldm=oldms;savm=savms;              pos += freq[jk][m][i];
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            if(pp[jk]>=1.e-10){
                    if(first==1){
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);              }
       fprintf(ficrest,"\n");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                    }else{
       hf=1;              if(first==1)
       if (stepm >= YEARM) hf=stepm/YEARM;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       epj=vector(1,nlstate+1);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       for(age=bage; age <=fage ;age++){            }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          }
         fprintf(ficrest," %.0f",age);  
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          for(jk=1; jk <=nlstate ; jk++){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];              pp[jk] += freq[jk][m][i];
           }          }       
           epj[nlstate+1] +=epj[j];          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         }            pos += pp[jk];
         for(i=1, vepp=0.;i <=nlstate;i++)            posprop += prop[jk][i];
           for(j=1;j <=nlstate;j++)          }
             vepp += vareij[i][j][(int)age];          for(jk=1; jk <=nlstate ; jk++){
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));            if(pos>=1.e-5){
         for(j=1;j <=nlstate;j++){              if(first==1)
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         fprintf(ficrest,"\n");            }else{
       }              if(first==1)
     }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                    }
  fclose(ficreseij);            if( i <= iagemax){
  fclose(ficresvij);              if(pos>=1.e-5){
   fclose(ficrest);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   fclose(ficpar);                /*probs[i][jk][j1]= pp[jk]/pos;*/
   free_vector(epj,1,nlstate+1);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   /*  scanf("%d ",i); */              }
               else
   /*------- Variance limit prevalence------*/                  fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
 strcpy(fileresvpl,"vpl");          }
   strcat(fileresvpl,fileres);          
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          for(jk=-1; jk <=nlstate+ndeath; jk++)
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);            for(m=-1; m <=nlstate+ndeath; m++)
     exit(0);              if(freq[jk][m][i] !=0 ) {
   }              if(first==1)
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
  k=0;              }
  for(cptcov=1;cptcov<=i1;cptcov++){          if(i <= iagemax)
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            fprintf(ficresp,"\n");
      k=k+1;          if(first==1)
      fprintf(ficresvpl,"\n#****** ");            printf("Others in log...\n");
      for(j=1;j<=cptcoveff;j++)          fprintf(ficlog,"\n");
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }
      fprintf(ficresvpl,"******\n");        /*}*/
          }
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    dateintmean=dateintsum/k2cpt; 
      oldm=oldms;savm=savms;   
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    fclose(ficresp);
    }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
  }    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   fclose(ficresvpl);    /* End of Freq */
   }
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  /************ Prevalence ********************/
    void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  {  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         in each health status at the date of interview (if between dateprev1 and dateprev2).
         We still use firstpass and lastpass as another selection.
   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);    int i, m, jk, j1, bool, z1,j;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  
      double **prop;
   free_matrix(matcov,1,npar,1,npar);    double posprop; 
   free_vector(delti,1,npar);    double  y2; /* in fractional years */
      int iagemin, iagemax;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    int first; /** to stop verbosity which is redirected to log file */
   
   printf("End of Imach\n");    iagemin= (int) agemin;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    iagemax= (int) agemax;
      /*pp=vector(1,nlstate);*/
   /* 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);*/    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   /*printf("Total time was %d uSec.\n", total_usecs);*/    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   /*------ End -----------*/    j1=0;
     
     /*j=cptcoveff;*/
  end:    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 #ifdef windows    
  chdir(pathcd);    first=1;
 #endif    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
  /*system("wgnuplot graph.plt");*/      /*for(i1=1; i1<=ncodemax[k1];i1++){
  /*system("../gp37mgw/wgnuplot graph.plt");*/        j1++;*/
  /*system("cd ../gp37mgw");*/        
  system("..\\gp37mgw\\wgnuplot graph.plt");        for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
 #ifdef windows            prop[i][m]=0.0;
   while (z[0] != 'q') {       
     chdir(pathcd);        for (i=1; i<=imx; i++) { /* Each individual */
     printf("\nType e to edit output files, c to start again, and q for exiting: ");          bool=1;
     scanf("%s",z);          if  (cptcovn>0) {
     if (z[0] == 'c') system("./imach");            for (z1=1; z1<=cptcoveff; z1++) 
     else if (z[0] == 'e') {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       chdir(path);                bool=0;
       system(optionfilehtm);          } 
     }          if (bool==1) { 
     else if (z[0] == 'q') exit(0);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
 #endif              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
               }
             } /* end selection of waves */
           }
         }
         for(i=iagemin; i <= iagemax+3; i++){  
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
           } 
           
           for(jk=1; jk <=nlstate ; jk++){     
             if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
               } else{
                 if(first==1){
                   first=0;
                   printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
                 }
               }
             } 
           }/* end jk */ 
         }/* end i */ 
       /*} *//* end i1 */
     } /* end j1 */
     
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   
   /************* Waves Concatenation ***************/
   
   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)
   {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        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]
        and mw[mi+1][i]. dh depends on stepm.
        */
   
     int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
     int first;
     int j, k=0,jk, ju, jl;
     double sum=0.;
     first=0;
     jmin=100000;
     jmax=-1;
     jmean=0.;
     for(i=1; i<=imx; i++){
       mi=0;
       m=firstpass;
       while(s[m][i] <= nlstate){
         if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           mw[++mi][i]=m;
         if(m >=lastpass)
           break;
         else
           m++;
       }/* end while */
       if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
         mw[mi][i]=m;
       }
   
       wav[i]=mi;
       if(mi==0){
         nbwarn++;
         if(first==0){
           printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           first=1;
         }
         if(first==1){
           fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         }
       } /* end mi==0 */
     } /* End individuals */
   
     for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
           dh[mi][i]=1;
         else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
                 nberr++;
                 printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 j=1; /* Temporary Dangerous patch */
                 printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                 fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               }
               k=k+1;
               if (j >= jmax){
                 jmax=j;
                 ijmax=i;
               }
               if (j <= jmin){
                 jmin=j;
                 ijmin=i;
               }
               sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
           }
           else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   
             k=k+1;
             if (j >= jmax) {
               jmax=j;
               ijmax=i;
             }
             else if (j <= jmin){
               jmin=j;
               ijmin=i;
             }
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             if(j<0){
               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;
           }
           jk= j/stepm;
           jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
               dh[mi][i]=jk;
               bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
                     * to avoid the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
             }
           }else{
             if(jl <= -ju){
               dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
                                    */
             }
             else{
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
             }
             if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
               /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             }
           } /* end if mle */
         }
       } /* end wave */
     }
     jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
     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);
    }
   
   /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   {
     /**< 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]= 
     */
   
     int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     int modmaxcovj=0; /* Modality max of covariates j */
     int cptcode=0; /* Modality max of covariates j */
     int modmincovj=0; /* Modality min of covariates j */
   
   
     cptcoveff=0; 
    
     for (k=-1; k < maxncov; k++) Ndum[k]=0;
     for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
     /* Loop on covariates without age and products */
     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 
                                  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 product of Vn*Vm, still boolean *:
                                       * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                                       * 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
                                         modality of the nth covariate of individual i. */
         if (ij > modmaxcovj)
           modmaxcovj=ij; 
         else if (ij < modmincovj) 
           modmincovj=ij; 
         if ((ij < -1) && (ij > NCOVMAX)){
           printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
           exit(1);
         }else
         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 */
         /*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
            female is 1, then modmaxcovj=1.*/
       }
       printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       cptcode=modmaxcovj;
       /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
      /*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 */
         printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
         if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
         }
         /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
            historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
       } /* Ndum[-1] number of undefined modalities */
   
       /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
       /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
       /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
          modmincovj=3; modmaxcovj = 7;
          There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
          which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
          variables V1_1 and V1_2.
          nbcode[Tvar[j]][ij]=k;
          nbcode[Tvar[j]][1]=0;
          nbcode[Tvar[j]][2]=1;
          nbcode[Tvar[j]][3]=2;
       */
       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 (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
           /*recode from 0 */
           if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
             nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                                        k is a modality. If we have model=V1+V1*sex 
                                        then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
             ij++;
           }
           if (ij > ncodemax[j]) break; 
         }  /* end of loop on */
       } /* 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*/  
     
    for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     
     for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
      /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
      ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
      Ndum[ij]++; 
    } 
   
    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)){
        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
        Tvaraff[ij]=i; /*For printing (unclear) */
        ij++;
      }else
          Tvaraff[ij]=0;
    }
    ij--;
    cptcoveff=ij; /*Number of total covariates*/
   
   }
   
   
   /*********** 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, no variances */
     int i, j, nhstepm, hstepm, h, nstepm;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3mat;
     double eip;
   
     pstamp(ficreseij);
     fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
         fprintf(ficreseij," e%1d%1d ",i,j);
       }
       fprintf(ficreseij," e%1d. ",i);
     }
     fprintf(ficreseij,"\n");
   
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        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 */ 
   
     agelim=AGESUP;
     /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       
   /* nhstepm age range expressed in number of stepm */
     nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     /* 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 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
     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 */
       
       hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       
       /* 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]);*/
   
           }
   
       fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0;
         for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
           fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
         fprintf(ficreseij,"%9.4f", eip );
       }
       fprintf(ficreseij,"\n");
       
     }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\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[] )
   
   {
     /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
     */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
     double *xp, *xm;
     double **gp, **gm;
     double ***gradg, ***trgradg;
     int theta;
   
     double eip, vip;
   
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
     xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
     pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
     }
     fprintf(ficresstdeij,"\n");
   
     pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(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,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
       }
     fprintf(ficrescveij,"\n");
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        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 from cross-sectional prevalence in each state (1 to %d) to period (stable) prevalence in specific state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int 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.1.12  
changed lines
  Added in v.1.165


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