Diff for /imach/src/imach.c between versions 1.41 and 1.164

version 1.41, 2002/05/07 15:53:01 version 1.164, 2014/12/16 10:52:11
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.164  2014/12/16 10:52:11  brouard
      Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    * imach.c (Module): Merging 1.61 to 1.162
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.163  2014/12/16 10:30:11  brouard
   case of a health survey which is our main interest) -2- at least a    * imach.c (Module): Merging 1.61 to 1.162
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.162  2014/09/25 11:43:39  brouard
   computed from the time spent in each health state according to a    Summary: temporary backup 0.99!
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.1  2014/09/16 11:06:58  brouard
   simplest model is the multinomial logistic model where pij is the    Summary: With some code (wrong) for nlopt
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Author:
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.161  2014/09/15 20:41:41  brouard
   complex model than "constant and age", you should modify the program    Summary: Problem with macro SQR on Intel compiler
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.160  2014/09/02 09:24:05  brouard
   convergence.    *** empty log message ***
   
   The advantage of this computer programme, compared to a simple    Revision 1.159  2014/09/01 10:34:10  brouard
   multinomial logistic model, is clear when the delay between waves is not    Summary: WIN32
   identical for each individual. Also, if a individual missed an    Author: Brouard
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.158  2014/08/27 17:11:51  brouard
     *** empty log message ***
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.157  2014/08/27 16:26:55  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    Summary: Preparing windows Visual studio version
   states. This elementary transition (by month or quarter trimester,    Author: Brouard
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    In order to compile on Visual studio, time.h is now correct and time_t
   and the contribution of each individual to the likelihood is simply    and tm struct should be used. difftime should be used but sometimes I
   hPijx.    just make the differences in raw time format (time(&now).
     Trying to suppress #ifdef LINUX
   Also this programme outputs the covariance matrix of the parameters but also    Add xdg-open for __linux in order to open default browser.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.156  2014/08/25 20:10:10  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 1.155  2014/08/25 18:32:34  brouard
   from the European Union.    Summary: New compile, minor changes
   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 .    Revision 1.154  2014/06/20 17:32:08  brouard
   **********************************************************************/    Summary: Outputs now all graphs of convergence to period prevalence
    
 #include <math.h>    Revision 1.153  2014/06/20 16:45:46  brouard
 #include <stdio.h>    Summary: If 3 live state, convergence to period prevalence on same graph
 #include <stdlib.h>    Author: Brouard
 #include <unistd.h>  
     Revision 1.152  2014/06/18 17:54:09  brouard
 #define MAXLINE 256    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 #define GNUPLOTPROGRAM "wgnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.151  2014/06/18 16:43:30  brouard
 #define FILENAMELENGTH 80    *** empty log message ***
 /*#define DEBUG*/  
 #define windows    Revision 1.150  2014/06/18 16:42:35  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Author: brouard
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.149  2014/06/18 15:51:14  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Summary: Some fixes in parameter files errors
     Author: Nicolas Brouard
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.148  2014/06/17 17:38:48  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Summary: Nothing new
 #define NCOVMAX 8 /* Maximum number of covariates */    Author: Brouard
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Just a new packaging for OS/X version 0.98nS
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.147  2014/06/16 10:33:11  brouard
     *** empty log message ***
   
 int erreur; /* Error number */    Revision 1.146  2014/06/16 10:20:28  brouard
 int nvar;    Summary: Merge
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Author: Brouard
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Merge, before building revised version.
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.145  2014/06/10 21:23:15  brouard
 int popbased=0;    Summary: Debugging with valgrind
     Author: Nicolas Brouard
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Lot of changes in order to output the results with some covariates
 int jmin, jmax; /* min, max spacing between 2 waves */    After the Edimburgh REVES conference 2014, it seems mandatory to
 int mle, weightopt;    improve the code.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    No more memory valgrind error but a lot has to be done in order to
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    continue the work of splitting the code into subroutines.
 double jmean; /* Mean space between 2 waves */    Also, decodemodel has been improved. Tricode is still not
 double **oldm, **newm, **savm; /* Working pointers to matrices */    optimal. nbcode should be improved. Documentation has been added in
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    the source code.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop;    Revision 1.143  2014/01/26 09:45:38  brouard
 FILE *ficreseij;    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   char fileresv[FILENAMELENGTH];    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.142  2014/01/26 03:57:36  brouard
     Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 #define NR_END 1  
 #define FREE_ARG char*    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define FTOL 1.0e-10  
     Revision 1.141  2014/01/26 02:42:01  brouard
 #define NRANSI    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define ITMAX 200  
     Revision 1.140  2011/09/02 10:37:54  brouard
 #define TOL 2.0e-4    Summary: times.h is ok with mingw32 now.
   
 #define CGOLD 0.3819660    Revision 1.139  2010/06/14 07:50:17  brouard
 #define ZEPS 1.0e-10    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   
 #define GOLD 1.618034    Revision 1.138  2010/04/30 18:19:40  brouard
 #define GLIMIT 100.0    *** empty log message ***
 #define TINY 1.0e-20  
     Revision 1.137  2010/04/29 18:11:38  brouard
 static double maxarg1,maxarg2;    (Module): Checking covariates for more complex models
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    than V1+V2. A lot of change to be done. Unstable.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.136  2010/04/26 20:30:53  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Module): merging some libgsl code. Fixing computation
 #define rint(a) floor(a+0.5)    of likelione (using inter/intrapolation if mle = 0) in order to
     get same likelihood as if mle=1.
 static double sqrarg;    Some cleaning of code and comments added.
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    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.
 int imx;  
 int stepm;    Revision 1.134  2009/10/29 13:18:53  brouard
 /* Stepm, step in month: minimum step interpolation*/    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
 int estepm;    Revision 1.133  2009/07/06 10:21:25  brouard
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    just nforces
   
 int m,nb;    Revision 1.132  2009/07/06 08:22:05  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Many tings
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.131  2009/06/20 16:22:47  brouard
 double dateintmean=0;    Some dimensions resccaled
   
 double *weight;    Revision 1.130  2009/05/26 06:44:34  brouard
 int **s; /* Status */    (Module): Max Covariate is now set to 20 instead of 8. A
 double *agedc, **covar, idx;    lot of cleaning with variables initialized to 0. Trying to make
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.129  2007/08/31 13:49:27  lievre
 double ftolhess; /* Tolerance for computing hessian */    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   
 /**************** split *************************/    Revision 1.128  2006/06/30 13:02:05  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    (Module): Clarifications on computing e.j
 {  
    char *s;                             /* pointer */    Revision 1.127  2006/04/28 18:11:50  brouard
    int  l1, l2;                         /* length counters */    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
    l1 = strlen( path );                 /* length of path */    loop. Now we define nhstepma in the age loop.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): In order to speed up (in case of numerous covariates) we
 #ifdef windows    compute health expectancies (without variances) in a first step
    s = strrchr( path, '\\' );           /* find last / */    and then all the health expectancies with variances or standard
 #else    deviation (needs data from the Hessian matrices) which slows the
    s = strrchr( path, '/' );            /* find last / */    computation.
 #endif    In the future we should be able to stop the program is only health
    if ( s == NULL ) {                   /* no directory, so use current */    expectancies and graph are needed without standard deviations.
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
       if ( getwd( dirc ) == NULL ) {    imach-114 because nhstepm was no more computed in the age
 #else    loop. Now we define nhstepma in the age loop.
       extern char       *getcwd( );    Version 0.98h
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.125  2006/04/04 15:20:31  lievre
 #endif    Errors in calculation of health expectancies. Age was not initialized.
          return( GLOCK_ERROR_GETCWD );    Forecasting file added.
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.124  2006/03/22 17:13:53  lievre
    } else {                             /* strip direcotry from path */    Parameters are printed with %lf instead of %f (more numbers after the comma).
       s++;                              /* after this, the filename */    The log-likelihood is printed in the log file
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.123  2006/03/20 10:52:43  brouard
       strcpy( name, s );                /* save file name */    * imach.c (Module): <title> changed, corresponds to .htm file
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    name. <head> headers where missing.
       dirc[l1-l2] = 0;                  /* add zero */  
    }    * imach.c (Module): Weights can have a decimal point as for
    l1 = strlen( dirc );                 /* length of directory */    English (a comma might work with a correct LC_NUMERIC environment,
 #ifdef windows    otherwise the weight is truncated).
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Modification of warning when the covariates values are not 0 or
 #else    1.
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Version 0.98g
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.122  2006/03/20 09:45:41  brouard
    s++;    (Module): Weights can have a decimal point as for
    strcpy(ext,s);                       /* save extension */    English (a comma might work with a correct LC_NUMERIC environment,
    l1= strlen( name);    otherwise the weight is truncated).
    l2= strlen( s)+1;    Modification of warning when the covariates values are not 0 or
    strncpy( finame, name, l1-l2);    1.
    finame[l1-l2]= 0;    Version 0.98g
    return( 0 );                         /* we're done */  
 }    Revision 1.121  2006/03/16 17:45:01  lievre
     * imach.c (Module): Comments concerning covariates added
   
 /******************************************/    * imach.c (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 void replace(char *s, char*t)    not 1 month. Version 0.98f
 {  
   int i;    Revision 1.120  2006/03/16 15:10:38  lievre
   int lg=20;    (Module): refinements in the computation of lli if
   i=0;    status=-2 in order to have more reliable computation if stepm is
   lg=strlen(t);    not 1 month. Version 0.98f
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.119  2006/03/15 17:42:26  brouard
     if (t[i]== '\\') s[i]='/';    (Module): Bug if status = -2, the loglikelihood was
   }    computed as likelihood omitting the logarithm. Version O.98e
 }  
     Revision 1.118  2006/03/14 18:20:07  brouard
 int nbocc(char *s, char occ)    (Module): varevsij Comments added explaining the second
 {    table of variances if popbased=1 .
   int i,j=0;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   int lg=20;    (Module): Function pstamp added
   i=0;    (Module): Version 0.98d
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.117  2006/03/14 17:16:22  brouard
   if  (s[i] == occ ) j++;    (Module): varevsij Comments added explaining the second
   }    table of variances if popbased=1 .
   return j;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 }    (Module): Function pstamp added
     (Module): Version 0.98d
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.116  2006/03/06 10:29:27  brouard
   int i,lg,j,p=0;    (Module): Variance-covariance wrong links and
   i=0;    varian-covariance of ej. is needed (Saito).
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Revision 1.115  2006/02/27 12:17:45  brouard
   }    (Module): One freematrix added in mlikeli! 0.98c
   
   lg=strlen(t);    Revision 1.114  2006/02/26 12:57:58  brouard
   for(j=0; j<p; j++) {    (Module): Some improvements in processing parameter
     (u[j] = t[j]);    filename with strsep.
   }  
      u[p]='\0';    Revision 1.113  2006/02/24 14:20:24  brouard
     (Module): Memory leaks checks with valgrind and:
    for(j=0; j<= lg; j++) {    datafile was not closed, some imatrix were not freed and on matrix
     if (j>=(p+1))(v[j-p-1] = t[j]);    allocation too.
   }  
 }    Revision 1.112  2006/01/30 09:55:26  brouard
     (Module): Back to gnuplot.exe instead of wgnuplot.exe
 /********************** nrerror ********************/  
     Revision 1.111  2006/01/25 20:38:18  brouard
 void nrerror(char error_text[])    (Module): Lots of cleaning and bugs added (Gompertz)
 {    (Module): Comments can be added in data file. Missing date values
   fprintf(stderr,"ERREUR ...\n");    can be a simple dot '.'.
   fprintf(stderr,"%s\n",error_text);  
   exit(1);    Revision 1.110  2006/01/25 00:51:50  brouard
 }    (Module): Lots of cleaning and bugs added (Gompertz)
 /*********************** vector *******************/  
 double *vector(int nl, int nh)    Revision 1.109  2006/01/24 19:37:15  brouard
 {    (Module): Comments (lines starting with a #) are allowed in data.
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.108  2006/01/19 18:05:42  lievre
   if (!v) nrerror("allocation failure in vector");    Gnuplot problem appeared...
   return v-nl+NR_END;    To be fixed
 }  
     Revision 1.107  2006/01/19 16:20:37  brouard
 /************************ free vector ******************/    Test existence of gnuplot in imach path
 void free_vector(double*v, int nl, int nh)  
 {    Revision 1.106  2006/01/19 13:24:36  brouard
   free((FREE_ARG)(v+nl-NR_END));    Some cleaning and links added in html output
 }  
     Revision 1.105  2006/01/05 20:23:19  lievre
 /************************ivector *******************************/    *** empty log message ***
 int *ivector(long nl,long nh)  
 {    Revision 1.104  2005/09/30 16:11:43  lievre
   int *v;    (Module): sump fixed, loop imx fixed, and simplifications.
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    (Module): If the status is missing at the last wave but we know
   if (!v) nrerror("allocation failure in ivector");    that the person is alive, then we can code his/her status as -2
   return v-nl+NR_END;    (instead of missing=-1 in earlier versions) and his/her
 }    contributions to the likelihood is 1 - Prob of dying from last
     health status (= 1-p13= p11+p12 in the easiest case of somebody in
 /******************free ivector **************************/    the healthy state at last known wave). Version is 0.98
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.103  2005/09/30 15:54:49  lievre
   free((FREE_ARG)(v+nl-NR_END));    (Module): sump fixed, loop imx fixed, and simplifications.
 }  
     Revision 1.102  2004/09/15 17:31:30  brouard
 /******************* imatrix *******************************/    Add the possibility to read data file including tab characters.
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Revision 1.101  2004/09/15 10:38:38  brouard
 {    Fix on curr_time
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    Revision 1.100  2004/07/12 18:29:06  brouard
      Add version for Mac OS X. Just define UNIX in Makefile
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Revision 1.99  2004/06/05 08:57:40  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    *** empty log message ***
   m += NR_END;  
   m -= nrl;    Revision 1.98  2004/05/16 15:05:56  brouard
      New version 0.97 . First attempt to estimate force of mortality
      directly from the data i.e. without the need of knowing the health
   /* allocate rows and set pointers to them */    state at each age, but using a Gompertz model: log u =a + b*age .
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    This is the basic analysis of mortality and should be done before any
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    other analysis, in order to test if the mortality estimated from the
   m[nrl] += NR_END;    cross-longitudinal survey is different from the mortality estimated
   m[nrl] -= ncl;    from other sources like vital statistic data.
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    The same imach parameter file can be used but the option for mle should be -3.
    
   /* return pointer to array of pointers to rows */    Agnès, who wrote this part of the code, tried to keep most of the
   return m;    former routines in order to include the new code within the former code.
 }  
     The output is very simple: only an estimate of the intercept and of
 /****************** free_imatrix *************************/    the slope with 95% confident intervals.
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    Current limitations:
       long nch,ncl,nrh,nrl;    A) Even if you enter covariates, i.e. with the
      /* free an int matrix allocated by imatrix() */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 {    B) There is no computation of Life Expectancy nor Life Table.
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Revision 1.97  2004/02/20 13:25:42  lievre
 }    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.96  2003/07/15 15:38:55  brouard
 {    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    rewritten within the same printf. Workaround: many printfs.
   double **m;  
     Revision 1.95  2003/07/08 07:54:34  brouard
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    * imach.c (Repository):
   if (!m) nrerror("allocation failure 1 in matrix()");    (Repository): Using imachwizard code to output a more meaningful covariance
   m += NR_END;    matrix (cov(a12,c31) instead of numbers.
   m -= nrl;  
     Revision 1.94  2003/06/27 13:00:02  brouard
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Just cleaning
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.93  2003/06/25 16:33:55  brouard
   m[nrl] -= ncl;    (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++) m[i]=m[i-1]+ncol;    (Module): Version 0.96b
   return m;  
 }    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 /*************************free matrix ************************/    exist so I changed back to asctime which exists.
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {    Revision 1.91  2003/06/25 15:30:29  brouard
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    * imach.c (Repository): Duplicated warning errors corrected.
   free((FREE_ARG)(m+nrl-NR_END));    (Repository): Elapsed time after each iteration is now output. It
 }    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
 /******************* ma3x *******************************/    concerning matrix of covariance. It has extension -cov.htm.
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {    Revision 1.90  2003/06/24 12:34:15  brouard
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    (Module): Some bugs corrected for windows. Also, when
   double ***m;    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.89  2003/06/24 12:30:52  brouard
   m += NR_END;    (Module): Some bugs corrected for windows. Also, when
   m -= nrl;    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.88  2003/06/23 17:54:56  brouard
   m[nrl] += NR_END;    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   m[nrl] -= ncl;  
     Revision 1.87  2003/06/18 12:26:01  brouard
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Version 0.96
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Revision 1.86  2003/06/17 20:04:08  brouard
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    (Module): Change position of html and gnuplot routines and added
   m[nrl][ncl] += NR_END;    routine fileappend.
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)    Revision 1.85  2003/06/17 13:12:43  brouard
     m[nrl][j]=m[nrl][j-1]+nlay;    * imach.c (Repository): Check when date of death was earlier that
      current date of interview. It may happen when the death was just
   for (i=nrl+1; i<=nrh; i++) {    prior to the death. In this case, dh was negative and likelihood
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    was wrong (infinity). We still send an "Error" but patch by
     for (j=ncl+1; j<=nch; j++)    assuming that the date of death was just one stepm after the
       m[i][j]=m[i][j-1]+nlay;    interview.
   }    (Repository): Because some people have very long ID (first column)
   return m;    we changed int to long in num[] and we added a new lvector for
 }    memory allocation. But we also truncated to 8 characters (left
     truncation)
 /*************************free ma3x ************************/    (Repository): No more line truncation errors.
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {    Revision 1.84  2003/06/13 21:44:43  brouard
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    * imach.c (Repository): Replace "freqsummary" at a correct
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    place. It differs from routine "prevalence" which may be called
   free((FREE_ARG)(m+nrl-NR_END));    many times. Probs is memory consuming and must be used with
 }    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 /***************** f1dim *************************/  
 extern int ncom;    Revision 1.83  2003/06/10 13:39:11  lievre
 extern double *pcom,*xicom;    *** empty log message ***
 extern double (*nrfunc)(double []);  
      Revision 1.82  2003/06/05 15:57:20  brouard
 double f1dim(double x)    Add log in  imach.c and  fullversion number is now printed.
 {  
   int j;  */
   double f;  /*
   double *xt;     Interpolated Markov Chain
    
   xt=vector(1,ncom);    Short summary of the programme:
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    
   f=(*nrfunc)(xt);    This program computes Healthy Life Expectancies from
   free_vector(xt,1,ncom);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   return f;    first survey ("cross") where individuals from different ages are
 }    interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
 /*****************brent *************************/    second wave of interviews ("longitudinal") which measure each change
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    (if any) in individual health status.  Health expectancies are
 {    computed from the time spent in each health state according to a
   int iter;    model. More health states you consider, more time is necessary to reach the
   double a,b,d,etemp;    Maximum Likelihood of the parameters involved in the model.  The
   double fu,fv,fw,fx;    simplest model is the multinomial logistic model where pij is the
   double ftemp;    probability to be observed in state j at the second wave
   double p,q,r,tol1,tol2,u,v,w,x,xm;    conditional to be observed in state i at the first wave. Therefore
   double e=0.0;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
      'age' is age and 'sex' is a covariate. If you want to have a more
   a=(ax < cx ? ax : cx);    complex model than "constant and age", you should modify the program
   b=(ax > cx ? ax : cx);    where the markup *Covariates have to be included here again* invites
   x=w=v=bx;    you to do it.  More covariates you add, slower the
   fw=fv=fx=(*f)(x);    convergence.
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);    The advantage of this computer programme, compared to a simple
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    multinomial logistic model, is clear when the delay between waves is not
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    identical for each individual. Also, if a individual missed an
     printf(".");fflush(stdout);    intermediate interview, the information is lost, but taken into
 #ifdef DEBUG    account using an interpolation or extrapolation.  
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    hPijx is the probability to be observed in state i at age x+h
 #endif    conditional to the observed state i at age x. The delay 'h' can be
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    split into an exact number (nh*stepm) of unobserved intermediate
       *xmin=x;    states. This elementary transition (by month, quarter,
       return fx;    semester or year) is modelled as a multinomial logistic.  The hPx
     }    matrix is simply the matrix product of nh*stepm elementary matrices
     ftemp=fu;    and the contribution of each individual to the likelihood is simply
     if (fabs(e) > tol1) {    hPijx.
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);    Also this programme outputs the covariance matrix of the parameters but also
       p=(x-v)*q-(x-w)*r;    of the life expectancies. It also computes the period (stable) prevalence. 
       q=2.0*(q-r);    
       if (q > 0.0) p = -p;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
       q=fabs(q);             Institut national d'études démographiques, Paris.
       etemp=e;    This software have been partly granted by Euro-REVES, a concerted action
       e=d;    from the European Union.
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    It is copyrighted identically to a GNU software product, ie programme and
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    software can be distributed freely for non commercial use. Latest version
       else {    can be accessed at http://euroreves.ined.fr/imach .
         d=p/q;  
         u=x+d;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
         if (u-a < tol2 || b-u < tol2)    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
           d=SIGN(tol1,xm-x);    
       }    **********************************************************************/
     } else {  /*
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    main
     }    read parameterfile
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    read datafile
     fu=(*f)(u);    concatwav
     if (fu <= fx) {    freqsummary
       if (u >= x) a=x; else b=x;    if (mle >= 1)
       SHFT(v,w,x,u)      mlikeli
         SHFT(fv,fw,fx,fu)    print results files
         } else {    if mle==1 
           if (u < x) a=u; else b=u;       computes hessian
           if (fu <= fw || w == x) {    read end of parameter file: agemin, agemax, bage, fage, estepm
             v=w;        begin-prev-date,...
             w=u;    open gnuplot file
             fv=fw;    open html file
             fw=fu;    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
           } else if (fu <= fv || v == x || v == w) {     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
             v=u;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
             fv=fu;      freexexit2 possible for memory heap.
           }  
         }    h Pij x                         | pij_nom  ficrestpij
   }     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   nrerror("Too many iterations in brent");         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
   *xmin=x;         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   return fx;  
 }         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
          1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
 /****************** mnbrak ***********************/    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
      Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
             double (*func)(double))  
 {    forecasting if prevfcast==1 prevforecast call prevalence()
   double ulim,u,r,q, dum;    health expectancies
   double fu;    Variance-covariance of DFLE
      prevalence()
   *fa=(*func)(*ax);     movingaverage()
   *fb=(*func)(*bx);    varevsij() 
   if (*fb > *fa) {    if popbased==1 varevsij(,popbased)
     SHFT(dum,*ax,*bx,dum)    total life expectancies
       SHFT(dum,*fb,*fa,dum)    Variance of period (stable) prevalence
       }   end
   *cx=(*bx)+GOLD*(*bx-*ax);  */
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);   
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #include <math.h>
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #include <stdio.h>
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #include <stdlib.h>
     if ((*bx-u)*(u-*cx) > 0.0) {  #include <string.h>
       fu=(*func)(u);  
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #ifdef _WIN32
       fu=(*func)(u);  #include <io.h>
       if (fu < *fc) {  #else
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #include <unistd.h>
           SHFT(*fb,*fc,fu,(*func)(u))  #endif
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  #include <limits.h>
       u=ulim;  #include <sys/types.h>
       fu=(*func)(u);  #include <sys/stat.h>
     } else {  #include <errno.h>
       u=(*cx)+GOLD*(*cx-*bx);  /* extern int errno; */
       fu=(*func)(u);  
     }  /* #ifdef LINUX */
     SHFT(*ax,*bx,*cx,u)  /* #include <time.h> */
       SHFT(*fa,*fb,*fc,fu)  /* #include "timeval.h" */
       }  /* #else */
 }  /* #include <sys/time.h> */
   /* #endif */
 /*************** linmin ************************/  
   #include <time.h>
 int ncom;  
 double *pcom,*xicom;  #ifdef GSL
 double (*nrfunc)(double []);  #include <gsl/gsl_errno.h>
    #include <gsl/gsl_multimin.h>
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  #endif
 {  
   double brent(double ax, double bx, double cx,  #ifdef NLOPT
                double (*f)(double), double tol, double *xmin);  #include <nlopt.h>
   double f1dim(double x);  typedef struct {
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    double (* function)(double [] );
               double *fc, double (*func)(double));  } myfunc_data ;
   int j;  #endif
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  /* #include <libintl.h> */
    /* #define _(String) gettext (String) */
   ncom=n;  
   pcom=vector(1,n);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   xicom=vector(1,n);  
   nrfunc=func;  #define GNUPLOTPROGRAM "gnuplot"
   for (j=1;j<=n;j++) {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     pcom[j]=p[j];  #define FILENAMELENGTH 132
     xicom[j]=xi[j];  
   }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   ax=0.0;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #define NINTERVMAX 8
 #endif  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
   for (j=1;j<=n;j++) {  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
     xi[j] *= xmin;  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
     p[j] += xi[j];  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
   }  #define MAXN 20000
   free_vector(xicom,1,n);  #define YEARM 12. /**< Number of months per year */
   free_vector(pcom,1,n);  #define AGESUP 130
 }  #define AGEBASE 40
   #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
 /*************** powell ************************/  #ifdef _WIN32
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #define DIRSEPARATOR '\\'
             double (*func)(double []))  #define CHARSEPARATOR "\\"
 {  #define ODIRSEPARATOR '/'
   void linmin(double p[], double xi[], int n, double *fret,  #else
               double (*func)(double []));  #define DIRSEPARATOR '/'
   int i,ibig,j;  #define CHARSEPARATOR "/"
   double del,t,*pt,*ptt,*xit;  #define ODIRSEPARATOR '\\'
   double fp,fptt;  #endif
   double *xits;  
   pt=vector(1,n);  /* $Id$ */
   ptt=vector(1,n);  /* $State$ */
   xit=vector(1,n);  
   xits=vector(1,n);  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)";
   *fret=(*func)(p);  char fullversion[]="$Revision$ $Date$"; 
   for (j=1;j<=n;j++) pt[j]=p[j];  char strstart[80];
   for (*iter=1;;++(*iter)) {  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
     fp=(*fret);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     ibig=0;  int nvar=0, nforce=0; /* Number of variables, number of forces */
     del=0.0;  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
     for (i=1;i<=n;i++)  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
       printf(" %d %.12f",i, p[i]);  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
     printf("\n");  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
     for (i=1;i<=n;i++) {  int cptcovprodnoage=0; /**< Number of covariate products without age */   
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  int cptcoveff=0; /* Total number of covariates to vary for printing results */
       fptt=(*fret);  int cptcov=0; /* Working variable */
 #ifdef DEBUG  int npar=NPARMAX;
       printf("fret=%lf \n",*fret);  int nlstate=2; /* Number of live states */
 #endif  int ndeath=1; /* Number of dead states */
       printf("%d",i);fflush(stdout);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       linmin(p,xit,n,fret,func);  int popbased=0;
       if (fabs(fptt-(*fret)) > del) {  
         del=fabs(fptt-(*fret));  int *wav; /* Number of waves for this individuual 0 is possible */
         ibig=i;  int maxwav=0; /* Maxim number of waves */
       }  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
 #ifdef DEBUG  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       printf("%d %.12e",i,(*fret));  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)*/
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  int mle=1, weightopt=0;
         printf(" x(%d)=%.12e",j,xit[j]);  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 */
       for(j=1;j<=n;j++)  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
         printf(" p=%.12e",p[j]);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       printf("\n");  int countcallfunc=0;  /* Count the number of calls to func */
 #endif  double jmean=1; /* Mean space between 2 waves */
     }  double **matprod2(); /* test */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  double **oldm, **newm, **savm; /* Working pointers to matrices */
 #ifdef DEBUG  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       int k[2],l;  /*FILE *fic ; */ /* Used in readdata only */
       k[0]=1;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       k[1]=-1;  FILE *ficlog, *ficrespow;
       printf("Max: %.12e",(*func)(p));  int globpr=0; /* Global variable for printing or not */
       for (j=1;j<=n;j++)  double fretone; /* Only one call to likelihood */
         printf(" %.12e",p[j]);  long ipmx=0; /* Number of contributions */
       printf("\n");  double sw; /* Sum of weights */
       for(l=0;l<=1;l++) {  char filerespow[FILENAMELENGTH];
         for (j=1;j<=n;j++) {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  FILE *ficresilk;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
         }  FILE *ficresprobmorprev;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  FILE *fichtm, *fichtmcov; /* Html File */
       }  FILE *ficreseij;
 #endif  char filerese[FILENAMELENGTH];
   FILE *ficresstdeij;
   char fileresstde[FILENAMELENGTH];
       free_vector(xit,1,n);  FILE *ficrescveij;
       free_vector(xits,1,n);  char filerescve[FILENAMELENGTH];
       free_vector(ptt,1,n);  FILE  *ficresvij;
       free_vector(pt,1,n);  char fileresv[FILENAMELENGTH];
       return;  FILE  *ficresvpl;
     }  char fileresvpl[FILENAMELENGTH];
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  char title[MAXLINE];
     for (j=1;j<=n;j++) {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       ptt[j]=2.0*p[j]-pt[j];  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       xit[j]=p[j]-pt[j];  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       pt[j]=p[j];  char command[FILENAMELENGTH];
     }  int  outcmd=0;
     fptt=(*func)(ptt);  
     if (fptt < fp) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {  char filelog[FILENAMELENGTH]; /* Log file */
         linmin(p,xit,n,fret,func);  char filerest[FILENAMELENGTH];
         for (j=1;j<=n;j++) {  char fileregp[FILENAMELENGTH];
           xi[j][ibig]=xi[j][n];  char popfile[FILENAMELENGTH];
           xi[j][n]=xit[j];  
         }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
         for(j=1;j<=n;j++)  /* struct timezone tzp; */
           printf(" %.12e",xit[j]);  /* extern int gettimeofday(); */
         printf("\n");  struct tm tml, *gmtime(), *localtime();
 #endif  
       }  extern time_t time();
     }  
   }  struct tm start_time, end_time, curr_time, last_time, forecast_time;
 }  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
   struct tm tm;
 /**** Prevalence limit ****************/  
   char strcurr[80], strfor[80];
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {  char *endptr;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  long lval;
      matrix by transitions matrix until convergence is reached */  double dval;
   
   int i, ii,j,k;  #define NR_END 1
   double min, max, maxmin, maxmax,sumnew=0.;  #define FREE_ARG char*
   double **matprod2();  #define FTOL 1.0e-10
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;  #define NRANSI 
   double agefin, delaymax=50 ; /* Max number of years to converge */  #define ITMAX 200 
   
   for (ii=1;ii<=nlstate+ndeath;ii++)  #define TOL 2.0e-4 
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  #define CGOLD 0.3819660 
     }  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
    cov[1]=1.;  
    #define GOLD 1.618034 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  #define GLIMIT 100.0 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  #define TINY 1.0e-20 
     newm=savm;  
     /* Covariates have to be included here again */  static double maxarg1,maxarg2;
      cov[2]=agefin;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       for (k=1; k<=cptcovn;k++) {    
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  #define rint(a) floor(a+0.5)
       }  
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  static double sqrarg;
       for (k=1; k<=cptcovprod;k++)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int agegomp= AGEGOMP;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  int imx; 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  int stepm=1;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  /* Stepm, step in month: minimum step interpolation*/
   
     savm=oldm;  int estepm;
     oldm=newm;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  int m,nb;
       min=1.;  long *num;
       max=0.;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       for(i=1; i<=nlstate; i++) {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
         sumnew=0;  double **pmmij, ***probs;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  double *ageexmed,*agecens;
         prlim[i][j]= newm[i][j]/(1-sumnew);  double dateintmean=0;
         max=FMAX(max,prlim[i][j]);  
         min=FMIN(min,prlim[i][j]);  double *weight;
       }  int **s; /* Status */
       maxmin=max-min;  double *agedc;
       maxmax=FMAX(maxmax,maxmin);  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
     }                    * covar=matrix(0,NCOVMAX,1,n); 
     if(maxmax < ftolpl){                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       return prlim;  double  idx; 
     }  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   }  int *Ndum; /** Freq of modality (tricode */
 }  int **codtab; /**< codtab=imatrix(1,100,1,10); */
   int **Tvard, *Tprod, cptcovprod, *Tvaraff;
 /*************** transition probabilities ***************/  double *lsurv, *lpop, *tpop;
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
 {  double ftolhess; /**< Tolerance for computing hessian */
   double s1, s2;  
   /*double t34;*/  /**************** split *************************/
   int i,j,j1, nc, ii, jj;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
     for(i=1; i<= nlstate; i++){    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     for(j=1; j<i;j++){       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    */ 
         /*s2 += param[i][j][nc]*cov[nc];*/    char  *ss;                            /* pointer */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    int   l1, l2;                         /* length counters */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }    l1 = strlen(path );                   /* length of path */
       ps[i][j]=s2;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     }    if ( ss == NULL ) {                   /* no directory, so determine current directory */
     for(j=i+1; j<=nlstate+ndeath;j++){      strcpy( name, path );               /* we got the fullname name because no directory */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      /* get current working directory */
       }      /*    extern  char* getcwd ( char *buf , int len);*/
       ps[i][j]=s2;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     }        return( GLOCK_ERROR_GETCWD );
   }      }
     /*ps[3][2]=1;*/      /* got dirc from getcwd*/
       printf(" DIRC = %s \n",dirc);
   for(i=1; i<= nlstate; i++){    } else {                              /* strip direcotry from path */
      s1=0;      ss++;                               /* after this, the filename */
     for(j=1; j<i; j++)      l2 = strlen( ss );                  /* length of filename */
       s1+=exp(ps[i][j]);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     for(j=i+1; j<=nlstate+ndeath; j++)      strcpy( name, ss );         /* save file name */
       s1+=exp(ps[i][j]);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     ps[i][i]=1./(s1+1.);      dirc[l1-l2] = 0;                    /* add zero */
     for(j=1; j<i; j++)      printf(" DIRC2 = %s \n",dirc);
       ps[i][j]= exp(ps[i][j])*ps[i][i];    }
     for(j=i+1; j<=nlstate+ndeath; j++)    /* We add a separator at the end of dirc if not exists */
       ps[i][j]= exp(ps[i][j])*ps[i][i];    l1 = strlen( dirc );                  /* length of directory */
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    if( dirc[l1-1] != DIRSEPARATOR ){
   } /* end i */      dirc[l1] =  DIRSEPARATOR;
       dirc[l1+1] = 0; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      printf(" DIRC3 = %s \n",dirc);
     for(jj=1; jj<= nlstate+ndeath; jj++){    }
       ps[ii][jj]=0;    ss = strrchr( name, '.' );            /* find last / */
       ps[ii][ii]=1;    if (ss >0){
     }      ss++;
   }      strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
       l2= strlen(ss)+1;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      strncpy( finame, name, l1-l2);
     for(jj=1; jj<= nlstate+ndeath; jj++){      finame[l1-l2]= 0;
      printf("%lf ",ps[ii][jj]);    }
    }  
     printf("\n ");    return( 0 );                          /* we're done */
     }  }
     printf("\n ");printf("%lf ",cov[2]);*/  
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  /******************************************/
   goto end;*/  
     return ps;  void replace_back_to_slash(char *s, char*t)
 }  {
     int i;
 /**************** Product of 2 matrices ******************/    int lg=0;
     i=0;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    lg=strlen(t);
 {    for(i=0; i<= lg; i++) {
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      (s[i] = t[i]);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      if (t[i]== '\\') s[i]='/';
   /* in, b, out are matrice of pointers which should have been initialized    }
      before: only the contents of out is modified. The function returns  }
      a pointer to pointers identical to out */  
   long i, j, k;  char *trimbb(char *out, char *in)
   for(i=nrl; i<= nrh; i++)  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     for(k=ncolol; k<=ncoloh; k++)    char *s;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    s=out;
         out[i][k] +=in[i][j]*b[j][k];    while (*in != '\0'){
       while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   return out;        in++;
 }      }
       *out++ = *in++;
     }
 /************* Higher Matrix Product ***************/    *out='\0';
     return s;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  }
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  char *cutl(char *blocc, char *alocc, char *in, char occ)
      duration (i.e. until  {
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
      (typically every 2 years instead of every month which is too big).       gives blocc="abcdef2ghi" and alocc="j".
      Model is determined by parameters x and covariates have to be       If occ is not found blocc is null and alocc is equal to in. Returns blocc
      included manually here.    */
     char *s, *t;
      */    t=in;s=in;
     while ((*in != occ) && (*in != '\0')){
   int i, j, d, h, k;      *alocc++ = *in++;
   double **out, cov[NCOVMAX];    }
   double **newm;    if( *in == occ){
       *(alocc)='\0';
   /* Hstepm could be zero and should return the unit matrix */      s=++in;
   for (i=1;i<=nlstate+ndeath;i++)    }
     for (j=1;j<=nlstate+ndeath;j++){   
       oldm[i][j]=(i==j ? 1.0 : 0.0);    if (s == t) {/* occ not found */
       po[i][j][0]=(i==j ? 1.0 : 0.0);      *(alocc-(in-s))='\0';
     }      in=s;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    }
   for(h=1; h <=nhstepm; h++){    while ( *in != '\0'){
     for(d=1; d <=hstepm; d++){      *blocc++ = *in++;
       newm=savm;    }
       /* Covariates have to be included here again */  
       cov[1]=1.;    *blocc='\0';
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    return t;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  }
       for (k=1; k<=cptcovage;k++)  char *cutv(char *blocc, char *alocc, char *in, char occ)
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  {
       for (k=1; k<=cptcovprod;k++)    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
        gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns alocc
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    char *s, *t;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    t=in;s=in;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    while (*in != '\0'){
       savm=oldm;      while( *in == occ){
       oldm=newm;        *blocc++ = *in++;
     }        s=in;
     for(i=1; i<=nlstate+ndeath; i++)      }
       for(j=1;j<=nlstate+ndeath;j++) {      *blocc++ = *in++;
         po[i][j][h]=newm[i][j];    }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    if (s == t) /* occ not found */
          */      *(blocc-(in-s))='\0';
       }    else
   } /* end h */      *(blocc-(in-s)-1)='\0';
   return po;    in=s;
 }    while ( *in != '\0'){
       *alocc++ = *in++;
     }
 /*************** log-likelihood *************/  
 double func( double *x)    *alocc='\0';
 {    return s;
   int i, ii, j, k, mi, d, kk;  }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;  int nbocc(char *s, char occ)
   double sw; /* Sum of weights */  {
   double lli; /* Individual log likelihood */    int i,j=0;
   long ipmx;    int lg=20;
   /*extern weight */    i=0;
   /* We are differentiating ll according to initial status */    lg=strlen(s);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    for(i=0; i<= lg; i++) {
   /*for(i=1;i<imx;i++)    if  (s[i] == occ ) j++;
     printf(" %d\n",s[4][i]);    }
   */    return j;
   cov[1]=1.;  }
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;  /* void cutv(char *u,char *v, char*t, char occ) */
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  /* { */
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
     for(mi=1; mi<= wav[i]-1; mi++){  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
       for (ii=1;ii<=nlstate+ndeath;ii++)  /*      gives u="abcdef2ghi" and v="j" *\/ */
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /*   int i,lg,j,p=0; */
       for(d=0; d<dh[mi][i]; d++){  /*   i=0; */
         newm=savm;  /*   lg=strlen(t); */
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  /*   for(j=0; j<=lg-1; j++) { */
         for (kk=1; kk<=cptcovage;kk++) {  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  /*   } */
         }  
          /*   for(j=0; j<p; j++) { */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  /*     (u[j] = t[j]); */
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  /*   } */
         savm=oldm;  /*      u[p]='\0'; */
         oldm=newm;  
          /*    for(j=0; j<= lg; j++) { */
          /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
       } /* end mult */  /*   } */
        /* } */
       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]]);*/  #ifdef _WIN32
       ipmx +=1;  char * strsep(char **pp, const char *delim)
       sw += weight[i];  {
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    char *p, *q;
     } /* end of wave */           
   } /* end of individual */    if ((p = *pp) == NULL)
       return 0;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    if ((q = strpbrk (p, delim)) != NULL)
   /* 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 */      *pp = q + 1;
   return -l;      *q = '\0';
 }    }
     else
       *pp = 0;
 /*********** Maximum Likelihood Estimation ***************/    return p;
   }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  #endif
 {  
   int i,j, iter;  /********************** nrerror ********************/
   double **xi,*delti;  
   double fret;  void nrerror(char error_text[])
   xi=matrix(1,npar,1,npar);  {
   for (i=1;i<=npar;i++)    fprintf(stderr,"ERREUR ...\n");
     for (j=1;j<=npar;j++)    fprintf(stderr,"%s\n",error_text);
       xi[i][j]=(i==j ? 1.0 : 0.0);    exit(EXIT_FAILURE);
   printf("Powell\n");  }
   powell(p,xi,npar,ftol,&iter,&fret,func);  /*********************** vector *******************/
   double *vector(int nl, int nh)
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  {
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 }    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
 /**** Computes Hessian and covariance matrix ***/  }
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  
 {  /************************ free vector ******************/
   double  **a,**y,*x,pd;  void free_vector(double*v, int nl, int nh)
   double **hess;  {
   int i, j,jk;    free((FREE_ARG)(v+nl-NR_END));
   int *indx;  }
   
   double hessii(double p[], double delta, int theta, double delti[]);  /************************ivector *******************************/
   double hessij(double p[], double delti[], int i, int j);  int *ivector(long nl,long nh)
   void lubksb(double **a, int npar, int *indx, double b[]) ;  {
   void ludcmp(double **a, int npar, int *indx, double *d) ;    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   hess=matrix(1,npar,1,npar);    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
   printf("\nCalculation of the hessian matrix. Wait...\n");  }
   for (i=1;i<=npar;i++){  
     printf("%d",i);fflush(stdout);  /******************free ivector **************************/
     hess[i][i]=hessii(p,ftolhess,i,delti);  void free_ivector(int *v, long nl, long nh)
     /*printf(" %f ",p[i]);*/  {
     /*printf(" %lf ",hess[i][i]);*/    free((FREE_ARG)(v+nl-NR_END));
   }  }
    
   for (i=1;i<=npar;i++) {  /************************lvector *******************************/
     for (j=1;j<=npar;j++)  {  long *lvector(long nl,long nh)
       if (j>i) {  {
         printf(".%d%d",i,j);fflush(stdout);    long *v;
         hess[i][j]=hessij(p,delti,i,j);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         hess[j][i]=hess[i][j];        if (!v) nrerror("allocation failure in ivector");
         /*printf(" %lf ",hess[i][j]);*/    return v-nl+NR_END;
       }  }
     }  
   }  /******************free lvector **************************/
   printf("\n");  void free_lvector(long *v, long nl, long nh)
   {
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    free((FREE_ARG)(v+nl-NR_END));
    }
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);  /******************* imatrix *******************************/
   x=vector(1,npar);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   indx=ivector(1,npar);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   for (i=1;i<=npar;i++)  { 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   ludcmp(a,npar,indx,&pd);    int **m; 
     
   for (j=1;j<=npar;j++) {    /* allocate pointers to rows */ 
     for (i=1;i<=npar;i++) x[i]=0;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     x[j]=1;    if (!m) nrerror("allocation failure 1 in matrix()"); 
     lubksb(a,npar,indx,x);    m += NR_END; 
     for (i=1;i<=npar;i++){    m -= nrl; 
       matcov[i][j]=x[i];    
     }    
   }    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   printf("\n#Hessian matrix#\n");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   for (i=1;i<=npar;i++) {    m[nrl] += NR_END; 
     for (j=1;j<=npar;j++) {    m[nrl] -= ncl; 
       printf("%.3e ",hess[i][j]);    
     }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     printf("\n");    
   }    /* return pointer to array of pointers to rows */ 
     return m; 
   /* Recompute Inverse */  } 
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  /****************** free_imatrix *************************/
   ludcmp(a,npar,indx,&pd);  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
   /*  printf("\n#Hessian matrix recomputed#\n");        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
   for (j=1;j<=npar;j++) {  { 
     for (i=1;i<=npar;i++) x[i]=0;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     x[j]=1;    free((FREE_ARG) (m+nrl-NR_END)); 
     lubksb(a,npar,indx,x);  } 
     for (i=1;i<=npar;i++){  
       y[i][j]=x[i];  /******************* matrix *******************************/
       printf("%.3e ",y[i][j]);  double **matrix(long nrl, long nrh, long ncl, long nch)
     }  {
     printf("\n");    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   }    double **m;
   */  
     m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   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);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 }    m[nrl] -= ncl;
   
 /*************** hessian matrix ****************/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 double hessii( double x[], double delta, int theta, double delti[])    return m;
 {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   int i;  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   int l=1, lmax=20;  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
   double k1,k2;     */
   double p2[NPARMAX+1];  }
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  /*************************free matrix ************************/
   double fx;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   int k=0,kmax=10;  {
   double l1;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
   fx=func(x);  }
   for (i=1;i<=npar;i++) p2[i]=x[i];  
   for(l=0 ; l <=lmax; l++){  /******************* ma3x *******************************/
     l1=pow(10,l);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     delts=delt;  {
     for(k=1 ; k <kmax; k=k+1){    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       delt = delta*(l1*k);    double ***m;
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       p2[theta]=x[theta]-delt;    if (!m) nrerror("allocation failure 1 in matrix()");
       k2=func(p2)-fx;    m += NR_END;
       /*res= (k1-2.0*fx+k2)/delt/delt; */    m -= nrl;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  
          m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 #ifdef DEBUG    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       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);    m[nrl] += NR_END;
 #endif    m[nrl] -= ncl;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         k=kmax;  
       }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         k=kmax; l=lmax*10.;    m[nrl][ncl] += NR_END;
       }    m[nrl][ncl] -= nll;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    for (j=ncl+1; j<=nch; j++) 
         delts=delt;      m[nrl][j]=m[nrl][j-1]+nlay;
       }    
     }    for (i=nrl+1; i<=nrh; i++) {
   }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   delti[theta]=delts;      for (j=ncl+1; j<=nch; j++) 
   return res;        m[i][j]=m[i][j-1]+nlay;
      }
 }    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 double hessij( double x[], double delti[], int thetai,int thetaj)             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 {    */
   int i;  }
   int l=1, l1, lmax=20;  
   double k1,k2,k3,k4,res,fx;  /*************************free ma3x ************************/
   double p2[NPARMAX+1];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   int k;  {
     free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   fx=func(x);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for (k=1; k<=2; k++) {    free((FREE_ARG)(m+nrl-NR_END));
     for (i=1;i<=npar;i++) p2[i]=x[i];  }
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /*************** function subdirf ***********/
     k1=func(p2)-fx;  char *subdirf(char fileres[])
    {
     p2[thetai]=x[thetai]+delti[thetai]/k;    /* Caution optionfilefiname is hidden */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    strcpy(tmpout,optionfilefiname);
     k2=func(p2)-fx;    strcat(tmpout,"/"); /* Add to the right */
      strcat(tmpout,fileres);
     p2[thetai]=x[thetai]-delti[thetai]/k;    return tmpout;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  }
     k3=func(p2)-fx;  
    /*************** function subdirf2 ***********/
     p2[thetai]=x[thetai]-delti[thetai]/k;  char *subdirf2(char fileres[], char *preop)
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  {
     k4=func(p2)-fx;    
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    /* Caution optionfilefiname is hidden */
 #ifdef DEBUG    strcpy(tmpout,optionfilefiname);
     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);    strcat(tmpout,"/");
 #endif    strcat(tmpout,preop);
   }    strcat(tmpout,fileres);
   return res;    return tmpout;
 }  }
   
 /************** Inverse of matrix **************/  /*************** function subdirf3 ***********/
 void ludcmp(double **a, int n, int *indx, double *d)  char *subdirf3(char fileres[], char *preop, char *preop2)
 {  {
   int i,imax,j,k;    
   double big,dum,sum,temp;    /* Caution optionfilefiname is hidden */
   double *vv;    strcpy(tmpout,optionfilefiname);
      strcat(tmpout,"/");
   vv=vector(1,n);    strcat(tmpout,preop);
   *d=1.0;    strcat(tmpout,preop2);
   for (i=1;i<=n;i++) {    strcat(tmpout,fileres);
     big=0.0;    return tmpout;
     for (j=1;j<=n;j++)  }
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  char *asc_diff_time(long time_sec, char ascdiff[])
     vv[i]=1.0/big;  {
   }    long sec_left, days, hours, minutes;
   for (j=1;j<=n;j++) {    days = (time_sec) / (60*60*24);
     for (i=1;i<j;i++) {    sec_left = (time_sec) % (60*60*24);
       sum=a[i][j];    hours = (sec_left) / (60*60) ;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    sec_left = (sec_left) %(60*60);
       a[i][j]=sum;    minutes = (sec_left) /60;
     }    sec_left = (sec_left) % (60);
     big=0.0;    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
     for (i=j;i<=n;i++) {    return ascdiff;
       sum=a[i][j];  }
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];  /***************** f1dim *************************/
       a[i][j]=sum;  extern int ncom; 
       if ( (dum=vv[i]*fabs(sum)) >= big) {  extern double *pcom,*xicom;
         big=dum;  extern double (*nrfunc)(double []); 
         imax=i;   
       }  double f1dim(double x) 
     }  { 
     if (j != imax) {    int j; 
       for (k=1;k<=n;k++) {    double f;
         dum=a[imax][k];    double *xt; 
         a[imax][k]=a[j][k];   
         a[j][k]=dum;    xt=vector(1,ncom); 
       }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       *d = -(*d);    f=(*nrfunc)(xt); 
       vv[imax]=vv[j];    free_vector(xt,1,ncom); 
     }    return f; 
     indx[j]=imax;  } 
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {  /*****************brent *************************/
       dum=1.0/(a[j][j]);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  { 
     }    int iter; 
   }    double a,b,d,etemp;
   free_vector(vv,1,n);  /* Doesn't work */    double fu=0,fv,fw,fx;
 ;    double ftemp=0.;
 }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
 void lubksb(double **a, int n, int *indx, double b[])   
 {    a=(ax < cx ? ax : cx); 
   int i,ii=0,ip,j;    b=(ax > cx ? ax : cx); 
   double sum;    x=w=v=bx; 
      fw=fv=fx=(*f)(x); 
   for (i=1;i<=n;i++) {    for (iter=1;iter<=ITMAX;iter++) { 
     ip=indx[i];      xm=0.5*(a+b); 
     sum=b[ip];      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     b[ip]=b[i];      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     if (ii)      printf(".");fflush(stdout);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      fprintf(ficlog,".");fflush(ficlog);
     else if (sum) ii=i;  #ifdef DEBUGBRENT
     b[i]=sum;      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);
   }      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   for (i=n;i>=1;i--) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     sum=b[i];  #endif
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     b[i]=sum/a[i][i];        *xmin=x; 
   }        return fx; 
 }      } 
       ftemp=fu;
 /************ Frequencies ********************/      if (fabs(e) > tol1) { 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)        r=(x-w)*(fx-fv); 
 {  /* Some frequencies */        q=(x-v)*(fx-fw); 
          p=(x-v)*q-(x-w)*r; 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        q=2.0*(q-r); 
   double ***freq; /* Frequencies */        if (q > 0.0) p = -p; 
   double *pp;        q=fabs(q); 
   double pos, k2, dateintsum=0,k2cpt=0;        etemp=e; 
   FILE *ficresp;        e=d; 
   char fileresp[FILENAMELENGTH];        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
            d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   pp=vector(1,nlstate);        else { 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          d=p/q; 
   strcpy(fileresp,"p");          u=x+d; 
   strcat(fileresp,fileres);          if (u-a < tol2 || b-u < tol2) 
   if((ficresp=fopen(fileresp,"w"))==NULL) {            d=SIGN(tol1,xm-x); 
     printf("Problem with prevalence resultfile: %s\n", fileresp);        } 
     exit(0);      } else { 
   }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      } 
   j1=0;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
        fu=(*f)(u); 
   j=cptcoveff;      if (fu <= fx) { 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        if (u >= x) a=x; else b=x; 
          SHFT(v,w,x,u) 
   for(k1=1; k1<=j;k1++){          SHFT(fv,fw,fx,fu) 
     for(i1=1; i1<=ncodemax[k1];i1++){          } else { 
       j1++;            if (u < x) a=u; else b=u; 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);            if (fu <= fw || w == x) { 
         scanf("%d", i);*/              v=w; 
       for (i=-1; i<=nlstate+ndeath; i++)                w=u; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)                fv=fw; 
           for(m=agemin; m <= agemax+3; m++)              fw=fu; 
             freq[i][jk][m]=0;            } else if (fu <= fv || v == x || v == w) { 
                    v=u; 
       dateintsum=0;              fv=fu; 
       k2cpt=0;            } 
       for (i=1; i<=imx; i++) {          } 
         bool=1;    } 
         if  (cptcovn>0) {    nrerror("Too many iterations in brent"); 
           for (z1=1; z1<=cptcoveff; z1++)    *xmin=x; 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    return fx; 
               bool=0;  } 
         }  
         if (bool==1) {  /****************** mnbrak ***********************/
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {              double (*func)(double)) 
               if(agev[m][i]==0) agev[m][i]=agemax+1;  { 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    double ulim,u,r,q, dum;
               if (m<lastpass) {    double fu; 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];   
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    *fa=(*func)(*ax); 
               }    *fb=(*func)(*bx); 
                  if (*fb > *fa) { 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      SHFT(dum,*ax,*bx,dum) 
                 dateintsum=dateintsum+k2;        SHFT(dum,*fb,*fa,dum) 
                 k2cpt++;        } 
               }    *cx=(*bx)+GOLD*(*bx-*ax); 
             }    *fc=(*func)(*cx); 
           }    while (*fb > *fc) { /* Declining fa, fb, fc */
         }      r=(*bx-*ax)*(*fb-*fc); 
       }      q=(*bx-*cx)*(*fb-*fa); 
              u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
       ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
       if  (cptcovn>0) {      if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
         fprintf(ficresp, "\n#********** Variable ");        fu=(*func)(u); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  #ifdef DEBUG
         fprintf(ficresp, "**********\n#");        /* f(x)=A(x-u)**2+f(u) */
       }        double A, fparabu; 
       for(i=1; i<=nlstate;i++)        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        fparabu= *fa - A*(*ax-u)*(*ax-u);
       fprintf(ficresp, "\n");        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);
       for(i=(int)agemin; i <= (int)agemax+3; i++){  #endif 
         if(i==(int)agemax+3)      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
           printf("Total");        fu=(*func)(u); 
         else        if (fu < *fc) { 
           printf("Age %d", i);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         for(jk=1; jk <=nlstate ; jk++){            SHFT(*fb,*fc,fu,(*func)(u)) 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            } 
             pp[jk] += freq[jk][m][i];      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
         }        u=ulim; 
         for(jk=1; jk <=nlstate ; jk++){        fu=(*func)(u); 
           for(m=-1, pos=0; m <=0 ; m++)      } else { 
             pos += freq[jk][m][i];        u=(*cx)+GOLD*(*cx-*bx); 
           if(pp[jk]>=1.e-10)        fu=(*func)(u); 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      } 
           else      SHFT(*ax,*bx,*cx,u) 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        SHFT(*fa,*fb,*fc,fu) 
         }        } 
   } 
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  /*************** linmin ************************/
             pp[jk] += freq[jk][m][i];  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
         }  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
   and replaces xi by the actual vector displacement that p was moved. Also returns as fret
         for(jk=1,pos=0; jk <=nlstate ; jk++)  the value of func at the returned location p . This is actually all accomplished by calling the
           pos += pp[jk];  routines mnbrak and brent .*/
         for(jk=1; jk <=nlstate ; jk++){  int ncom; 
           if(pos>=1.e-5)  double *pcom,*xicom;
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  double (*nrfunc)(double []); 
           else   
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
           if( i <= (int) agemax){  { 
             if(pos>=1.e-5){    double brent(double ax, double bx, double cx, 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);                 double (*f)(double), double tol, double *xmin); 
               probs[i][jk][j1]= pp[jk]/pos;    double f1dim(double x); 
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
             }                double *fc, double (*func)(double)); 
             else    int j; 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    double xx,xmin,bx,ax; 
           }    double fx,fb,fa;
         }   
            ncom=n; 
         for(jk=-1; jk <=nlstate+ndeath; jk++)    pcom=vector(1,n); 
           for(m=-1; m <=nlstate+ndeath; m++)    xicom=vector(1,n); 
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    nrfunc=func; 
         if(i <= (int) agemax)    for (j=1;j<=n;j++) { 
           fprintf(ficresp,"\n");      pcom[j]=p[j]; 
         printf("\n");      xicom[j]=xi[j]; 
       }    } 
     }    ax=0.0; 
   }    xx=1.0; 
   dateintmean=dateintsum/k2cpt;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
      *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
   fclose(ficresp);  #ifdef DEBUG
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   free_vector(pp,1,nlstate);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
    #endif
   /* End of Freq */    for (j=1;j<=n;j++) { 
 }      xi[j] *= xmin; 
       p[j] += xi[j]; 
 /************ Prevalence ********************/    } 
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    free_vector(xicom,1,n); 
 {  /* Some frequencies */    free_vector(pcom,1,n); 
    } 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */  
   double *pp;  /*************** powell ************************/
   double pos, k2;  /*
   Minimization of a function func of n variables. Input consists of an initial starting point
   pp=vector(1,nlstate);  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
    such that failure to decrease by more than this amount on one iteration signals doneness. On
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
   j1=0;  function value at p , and iter is the number of iterations taken. The routine linmin is used.
     */
   j=cptcoveff;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}              double (*func)(double [])) 
    { 
  for(k1=1; k1<=j;k1++){    void linmin(double p[], double xi[], int n, double *fret, 
     for(i1=1; i1<=ncodemax[k1];i1++){                double (*func)(double [])); 
       j1++;    int i,ibig,j; 
      double del,t,*pt,*ptt,*xit;
       for (i=-1; i<=nlstate+ndeath; i++)      double fp,fptt;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      double *xits;
           for(m=agemin; m <= agemax+3; m++)    int niterf, itmp;
             freq[i][jk][m]=0;  
          pt=vector(1,n); 
       for (i=1; i<=imx; i++) {    ptt=vector(1,n); 
         bool=1;    xit=vector(1,n); 
         if  (cptcovn>0) {    xits=vector(1,n); 
           for (z1=1; z1<=cptcoveff; z1++)    *fret=(*func)(p); 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    for (j=1;j<=n;j++) pt[j]=p[j]; 
               bool=0;      rcurr_time = time(NULL);  
         }    for (*iter=1;;++(*iter)) { 
         if (bool==1) {      fp=(*fret); 
           for(m=firstpass; m<=lastpass; m++){      ibig=0; 
             k2=anint[m][i]+(mint[m][i]/12.);      del=0.0; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      rlast_time=rcurr_time;
               if(agev[m][i]==0) agev[m][i]=agemax+1;      /* (void) gettimeofday(&curr_time,&tzp); */
               if(agev[m][i]==1) agev[m][i]=agemax+2;      rcurr_time = time(NULL);  
               if (m<lastpass)      curr_time = *localtime(&rcurr_time);
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
               else      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];     for (i=1;i<=n;i++) {
             }        printf(" %d %.12f",i, p[i]);
           }        fprintf(ficlog," %d %.12lf",i, p[i]);
         }        fprintf(ficrespow," %.12lf", p[i]);
       }      }
         for(i=(int)agemin; i <= (int)agemax+3; i++){      printf("\n");
           for(jk=1; jk <=nlstate ; jk++){      fprintf(ficlog,"\n");
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      fprintf(ficrespow,"\n");fflush(ficrespow);
               pp[jk] += freq[jk][m][i];      if(*iter <=3){
           }        tml = *localtime(&rcurr_time);
           for(jk=1; jk <=nlstate ; jk++){        strcpy(strcurr,asctime(&tml));
             for(m=-1, pos=0; m <=0 ; m++)        rforecast_time=rcurr_time; 
             pos += freq[jk][m][i];        itmp = strlen(strcurr);
         }        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
                  strcurr[itmp-1]='\0';
          for(jk=1; jk <=nlstate ; jk++){        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
              pp[jk] += freq[jk][m][i];        for(niterf=10;niterf<=30;niterf+=10){
          }          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
                    forecast_time = *localtime(&rforecast_time);
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          strcpy(strfor,asctime(&forecast_time));
           itmp = strlen(strfor);
          for(jk=1; jk <=nlstate ; jk++){                    if(strfor[itmp-1]=='\n')
            if( i <= (int) agemax){          strfor[itmp-1]='\0';
              if(pos>=1.e-5){          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);
                probs[i][jk][j1]= pp[jk]/pos;          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);
              }        }
            }      }
          }      for (i=1;i<=n;i++) { 
                  for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         }        fptt=(*fret); 
     }  #ifdef DEBUG
   }            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
             fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
    #endif
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        printf("%d",i);fflush(stdout);
   free_vector(pp,1,nlstate);        fprintf(ficlog,"%d",i);fflush(ficlog);
          linmin(p,xit,n,fret,func); 
 }  /* End of Freq */        if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
 /************* Waves Concatenation ***************/          ibig=i; 
         } 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  #ifdef DEBUG
 {        printf("%d %.12e",i,(*fret));
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        fprintf(ficlog,"%d %.12e",i,(*fret));
      Death is a valid wave (if date is known).        for (j=1;j<=n;j++) {
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          printf(" x(%d)=%.12e",j,xit[j]);
      and mw[mi+1][i]. dh depends on stepm.          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
      */        }
         for(j=1;j<=n;j++) {
   int i, mi, m;          printf(" p(%d)=%.12e",j,p[j]);
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
      double sum=0., jmean=0.;*/        }
         printf("\n");
   int j, k=0,jk, ju, jl;        fprintf(ficlog,"\n");
   double sum=0.;  #endif
   jmin=1e+5;      } /* end i */
   jmax=-1;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   jmean=0.;  #ifdef DEBUG
   for(i=1; i<=imx; i++){        int k[2],l;
     mi=0;        k[0]=1;
     m=firstpass;        k[1]=-1;
     while(s[m][i] <= nlstate){        printf("Max: %.12e",(*func)(p));
       if(s[m][i]>=1)        fprintf(ficlog,"Max: %.12e",(*func)(p));
         mw[++mi][i]=m;        for (j=1;j<=n;j++) {
       if(m >=lastpass)          printf(" %.12e",p[j]);
         break;          fprintf(ficlog," %.12e",p[j]);
       else        }
         m++;        printf("\n");
     }/* end while */        fprintf(ficlog,"\n");
     if (s[m][i] > nlstate){        for(l=0;l<=1;l++) {
       mi++;     /* Death is another wave */          for (j=1;j<=n;j++) {
       /* if(mi==0)  never been interviewed correctly before death */            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
          /* Only death is a correct wave */            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       mw[mi][i]=m;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     }          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     wav[i]=mi;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     if(mi==0)        }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  #endif
   }  
   
   for(i=1; i<=imx; i++){        free_vector(xit,1,n); 
     for(mi=1; mi<wav[i];mi++){        free_vector(xits,1,n); 
       if (stepm <=0)        free_vector(ptt,1,n); 
         dh[mi][i]=1;        free_vector(pt,1,n); 
       else{        return; 
         if (s[mw[mi+1][i]][i] > nlstate) {      } 
           if (agedc[i] < 2*AGESUP) {      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
           if(j==0) j=1;  /* Survives at least one month after exam */        ptt[j]=2.0*p[j]-pt[j]; 
           k=k+1;        xit[j]=p[j]-pt[j]; 
           if (j >= jmax) jmax=j;        pt[j]=p[j]; 
           if (j <= jmin) jmin=j;      } 
           sum=sum+j;      fptt=(*func)(ptt); 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
           }        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
         }        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
         else{        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
           k=k+1;        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
           if (j >= jmax) jmax=j;        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
           else if (j <= jmin)jmin=j;        /* Thus we compare delta(2h) with observed f1-f3 */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        /* or best gain on one ancient line 'del' with total  */
           sum=sum+j;        /* gain f1-f2 = f1 - f2 - 'del' with del  */
         }        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
         jk= j/stepm;  
         jl= j -jk*stepm;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
         ju= j -(jk+1)*stepm;        t= t- del*SQR(fp-fptt);
         if(jl <= -ju)        printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
           dh[mi][i]=jk;        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);
         else  #ifdef DEBUG
           dh[mi][i]=jk+1;        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
         if(dh[mi][i]==0)               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
           dh[mi][i]=1; /* At least one step */        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
       }               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
     }        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);
   }        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);
   jmean=sum/k;  #endif
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        if (t < 0.0) { /* Then we use it for last direction */
  }          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
 /*********** Tricode ****************************/          for (j=1;j<=n;j++) { 
 void tricode(int *Tvar, int **nbcode, int imx)            xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
 {            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
   int Ndum[20],ij=1, k, j, i;          }
   int cptcode=0;          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   cptcoveff=0;          fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
    
   for (k=0; k<19; k++) Ndum[k]=0;  #ifdef DEBUG
   for (k=1; k<=7; k++) ncodemax[k]=0;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          for(j=1;j<=n;j++){
     for (i=1; i<=imx; i++) {            printf(" %.12e",xit[j]);
       ij=(int)(covar[Tvar[j]][i]);            fprintf(ficlog," %.12e",xit[j]);
       Ndum[ij]++;          }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          printf("\n");
       if (ij > cptcode) cptcode=ij;          fprintf(ficlog,"\n");
     }  #endif
         } /* end of t negative */
     for (i=0; i<=cptcode; i++) {      } /* end if (fptt < fp)  */
       if(Ndum[i]!=0) ncodemax[j]++;    } 
     }  } 
     ij=1;  
   /**** Prevalence limit (stable or period prevalence)  ****************/
   
     for (i=1; i<=ncodemax[j]; i++) {  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       for (k=0; k<=19; k++) {  {
         if (Ndum[k] != 0) {    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
           nbcode[Tvar[j]][ij]=k;       matrix by transitions matrix until convergence is reached */
            
           ij++;    int i, ii,j,k;
         }    double min, max, maxmin, maxmax,sumnew=0.;
         if (ij > ncodemax[j]) break;    /* double **matprod2(); */ /* test */
       }      double **out, cov[NCOVMAX+1], **pmij();
     }    double **newm;
   }      double agefin, delaymax=50 ; /* Max number of years to converge */
   
  for (k=0; k<19; k++) Ndum[k]=0;    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
  for (i=1; i<=ncovmodel-2; i++) {        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       ij=Tvar[i];      }
       Ndum[ij]++;  
     }     cov[1]=1.;
    
  ij=1;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
  for (i=1; i<=10; i++) {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
    if((Ndum[i]!=0) && (i<=ncovcol)){      newm=savm;
      Tvaraff[ij]=i;      /* Covariates have to be included here again */
      ij++;      cov[2]=agefin;
    }      
  }      for (k=1; k<=cptcovn;k++) {
          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     cptcoveff=ij-1;        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
 }      }
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
 /*********** Health Expectancies ****************/      /* 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]]]; */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )      
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
 {      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   /* Health expectancies */      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   double age, agelim, hf;      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
   double ***p3mat,***varhe;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
   double **dnewm,**doldm;      
   double *xp;      savm=oldm;
   double **gp, **gm;      oldm=newm;
   double ***gradg, ***trgradg;      maxmax=0.;
   int theta;      for(j=1;j<=nlstate;j++){
         min=1.;
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);        max=0.;
   xp=vector(1,npar);        for(i=1; i<=nlstate; i++) {
   dnewm=matrix(1,nlstate*2,1,npar);          sumnew=0;
   doldm=matrix(1,nlstate*2,1,nlstate*2);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
            prlim[i][j]= newm[i][j]/(1-sumnew);
   fprintf(ficreseij,"# Health expectancies\n");          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
   fprintf(ficreseij,"# Age");          max=FMAX(max,prlim[i][j]);
   for(i=1; i<=nlstate;i++)          min=FMIN(min,prlim[i][j]);
     for(j=1; j<=nlstate;j++)        }
       fprintf(ficreseij," %1d-%1d (SE)",i,j);        maxmin=max-min;
   fprintf(ficreseij,"\n");        maxmax=FMAX(maxmax,maxmin);
       }
   if(estepm < stepm){      if(maxmax < ftolpl){
     printf ("Problem %d lower than %d\n",estepm, stepm);        return prlim;
   }      }
   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  /*************** transition probabilities ***************/ 
    * we are calculating an estimate of the Life Expectancy assuming a linear  
    * progression inbetween and thus overestimating or underestimating according  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
    * 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    /* According to parameters values stored in x and the covariate's values stored in cov,
    * to compare the new estimate of Life expectancy with the same linear       computes the probability to be observed in state j being in state i by appying the
    * hypothesis. A more precise result, taking into account a more precise       model to the ncovmodel covariates (including constant and age).
    * curvature will be obtained if estepm is as small as stepm. */       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
        and, according on how parameters are entered, the position of the coefficient xij(nc) of the
   /* For example we decided to compute the life expectancy with the smallest unit */       ncth covariate in the global vector x is given by the formula:
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
      nhstepm is the number of hstepm from age to agelim       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
      nstepm is the number of stepm from age to agelin.       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
      Look at hpijx to understand the reason of that which relies in memory size       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
      and note for a fixed period like estepm months */       Outputs ps[i][j] the probability to be observed in j being in j according to
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
      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    double s1, lnpijopii;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    /*double t34;*/
      results. So we changed our mind and took the option of the best precision.    int i,j, nc, ii, jj;
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      for(i=1; i<= nlstate; i++){
         for(j=1; j<i;j++){
   agelim=AGESUP;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            /*lnpijopii += param[i][j][nc]*cov[nc];*/
     /* nhstepm age range expressed in number of stepm */            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          }
     /* if (stepm >= YEARM) hstepm=1;*/          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);        for(j=i+1; j<=nlstate+ndeath;j++){
     gp=matrix(0,nhstepm,1,nlstate*2);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     gm=matrix(0,nhstepm,1,nlstate*2);            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
             lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
          }
       }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      
       for(i=1; i<= nlstate; i++){
     /* Computing Variances of health expectancies */        s1=0;
         for(j=1; j<i; j++){
      for(theta=1; theta <=npar; theta++){          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       for(i=1; i<=npar; i++){          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        }
       }        for(j=i+1; j<=nlstate+ndeath; j++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            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); */
       cptj=0;        }
       for(j=1; j<= nlstate; j++){        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
         for(i=1; i<=nlstate; i++){        ps[i][i]=1./(s1+1.);
           cptj=cptj+1;        /* Computing other pijs */
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){        for(j=1; j<i; j++)
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          ps[i][j]= exp(ps[i][j])*ps[i][i];
           }        for(j=i+1; j<=nlstate+ndeath; j++)
         }          ps[i][j]= exp(ps[i][j])*ps[i][i];
       }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
            } /* end i */
            
       for(i=1; i<=npar; i++)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for(jj=1; jj<= nlstate+ndeath; jj++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            ps[ii][jj]=0;
                ps[ii][ii]=1;
       cptj=0;        }
       for(j=1; j<= nlstate; j++){      }
         for(i=1;i<=nlstate;i++){      
           cptj=cptj+1;      
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
           }      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
         }      /*   } */
       }      /*   printf("\n "); */
            /* } */
          /* printf("\n ");printf("%lf ",cov[2]);*/
       /*
       for(j=1; j<= nlstate*2; j++)        for(i=1; i<= npar; i++) printf("%f ",x[i]);
         for(h=0; h<=nhstepm-1; h++){        goto end;*/
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      return ps;
         }  }
   
      }  /**************** Product of 2 matrices ******************/
      
 /* End theta */  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   {
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
        b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
      for(h=0; h<=nhstepm-1; h++)    /* in, b, out are matrice of pointers which should have been initialized 
       for(j=1; j<=nlstate*2;j++)       before: only the contents of out is modified. The function returns
         for(theta=1; theta <=npar; theta++)       a pointer to pointers identical to out */
         trgradg[h][j][theta]=gradg[h][theta][j];    int i, j, k;
     for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++){
      for(i=1;i<=nlstate*2;i++)        out[i][k]=0.;
       for(j=1;j<=nlstate*2;j++)        for(j=ncl; j<=nch; j++)
         varhe[i][j][(int)age] =0.;          out[i][k] +=in[i][j]*b[j][k];
       }
     for(h=0;h<=nhstepm-1;h++){    return out;
       for(k=0;k<=nhstepm-1;k++){  }
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);  
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);  
         for(i=1;i<=nlstate*2;i++)  /************* Higher Matrix Product ***************/
           for(j=1;j<=nlstate*2;j++)  
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       }  {
     }    /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
             age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     /* Computing expectancies */       nhstepm*hstepm matrices. 
     for(i=1; i<=nlstate;i++)       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       for(j=1; j<=nlstate;j++)       (typically every 2 years instead of every month which is too big 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){       for the memory).
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;       Model is determined by parameters x and covariates have to be 
                 included manually here. 
 /* 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]);*/  
        */
         }  
     int i, j, d, h, k;
     fprintf(ficreseij,"%3.0f",age );    double **out, cov[NCOVMAX+1];
     cptj=0;    double **newm;
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){    /* Hstepm could be zero and should return the unit matrix */
         cptj++;    for (i=1;i<=nlstate+ndeath;i++)
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      for (j=1;j<=nlstate+ndeath;j++){
       }        oldm[i][j]=(i==j ? 1.0 : 0.0);
     fprintf(ficreseij,"\n");        po[i][j][0]=(i==j ? 1.0 : 0.0);
          }
     free_matrix(gm,0,nhstepm,1,nlstate*2);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     free_matrix(gp,0,nhstepm,1,nlstate*2);    for(h=1; h <=nhstepm; h++){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);      for(d=1; d <=hstepm; d++){
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);        newm=savm;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* Covariates have to be included here again */
   }        cov[1]=1.;
   free_vector(xp,1,npar);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   free_matrix(dnewm,1,nlstate*2,1,npar);        for (k=1; k<=cptcovn;k++) 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);        for (k=1; k<=cptcovage;k++)
 }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
 /************ Variance ******************/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)  
 {  
   /* Variance of health expectancies */        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   double **newm;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   double **dnewm,**doldm;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   int i, j, nhstepm, hstepm, h, nstepm ;        savm=oldm;
   int k, cptcode;        oldm=newm;
   double *xp;      }
   double **gp, **gm;      for(i=1; i<=nlstate+ndeath; i++)
   double ***gradg, ***trgradg;        for(j=1;j<=nlstate+ndeath;j++) {
   double ***p3mat;          po[i][j][h]=newm[i][j];
   double age,agelim, hf;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   int theta;        }
       /*printf("h=%d ",h);*/
    fprintf(ficresvij,"# Covariances of life expectancies\n");    } /* end h */
   fprintf(ficresvij,"# Age");  /*     printf("\n H=%d \n",h); */
   for(i=1; i<=nlstate;i++)    return po;
     for(j=1; j<=nlstate;j++)  }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  
   fprintf(ficresvij,"\n");  #ifdef NLOPT
     double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
   xp=vector(1,npar);    double fret;
   dnewm=matrix(1,nlstate,1,npar);    double *xt;
   doldm=matrix(1,nlstate,1,nlstate);    int j;
      myfunc_data *d2 = (myfunc_data *) pd;
   if(estepm < stepm){  /* xt = (p1-1); */
     printf ("Problem %d lower than %d\n",estepm, stepm);    xt=vector(1,n); 
   }    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
   else  hstepm=estepm;    
   /* For example we decided to compute the life expectancy with the smallest unit */    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
      nhstepm is the number of hstepm from age to agelim    printf("Function = %.12lf ",fret);
      nstepm is the number of stepm from age to agelin.    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
      Look at hpijx to understand the reason of that which relies in memory size    printf("\n");
      and note for a fixed period like k years */   free_vector(xt,1,n);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    return fret;
      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  #endif
      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.  /*************** log-likelihood *************/
   */  double func( double *x)
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  {
   agelim = AGESUP;    int i, ii, j, k, mi, d, kk;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double **out;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    double sw; /* Sum of weights */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double lli; /* Individual log likelihood */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    int s1, s2;
     gp=matrix(0,nhstepm,1,nlstate);    double bbh, survp;
     gm=matrix(0,nhstepm,1,nlstate);    long ipmx;
     /*extern weight */
     for(theta=1; theta <=npar; theta++){    /* We are differentiating ll according to initial status */
       for(i=1; i<=npar; i++){ /* Computes gradient */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /*for(i=1;i<imx;i++) 
       }      printf(" %d\n",s[4][i]);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
     ++countcallfunc;
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)    cov[1]=1.;
           prlim[i][i]=probs[(int)age][i][ij];  
       }    for(k=1; k<=nlstate; k++) ll[k]=0.;
    
       for(j=1; j<= nlstate; j++){    if(mle==1){
         for(h=0; h<=nhstepm; h++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        /* Computes the values of the ncovmodel covariates of the model
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];           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
       }           to be observed in j being in i according to the model.
             */
       for(i=1; i<=npar; i++) /* Computes gradient */        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          cov[2+k]=covar[Tvar[k]][i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
             is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
       if (popbased==1) {           has been calculated etc */
         for(i=1; i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
           prlim[i][i]=probs[(int)age][i][ij];          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<= nlstate; j++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(h=0; h<=nhstepm; h++){            }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          for(d=0; d<dh[mi][i]; d++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
       for(j=1; j<= nlstate; j++)            }
         for(h=0; h<=nhstepm; h++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
     } /* End theta */            oldm=newm;
           } /* end mult */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     for(h=0; h<=nhstepm; h++)          /* But now since version 0.9 we anticipate for bias at large stepm.
       for(j=1; j<=nlstate;j++)           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         for(theta=1; theta <=npar; theta++)           * (in months) between two waves is not a multiple of stepm, we rounded to 
           trgradg[h][j][theta]=gradg[h][theta][j];           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
     for(i=1;i<=nlstate;i++)           * probability in order to take into account the bias as a fraction of the way
       for(j=1;j<=nlstate;j++)           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         vareij[i][j][(int)age] =0.;           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
     for(h=0;h<=nhstepm;h++){           * For stepm > 1 the results are less biased than in previous versions. 
       for(k=0;k<=nhstepm;k++){           */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          s1=s[mw[mi][i]][i];
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          s2=s[mw[mi+1][i]][i];
         for(i=1;i<=nlstate;i++)          bbh=(double)bh[mi][i]/(double)stepm; 
           for(j=1;j<=nlstate;j++)          /* bias bh is positive if real duration
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;           * is higher than the multiple of stepm and negative otherwise.
       }           */
     }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           if( s2 > nlstate){ 
     fprintf(ficresvij,"%.0f ",age );            /* i.e. if s2 is a death state and if the date of death is known 
     for(i=1; i<=nlstate;i++)               then the contribution to the likelihood is the probability to 
       for(j=1; j<=nlstate;j++){               die between last step unit time and current  step unit time, 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);               which is also equal to probability to die before dh 
       }               minus probability to die before dh-stepm . 
     fprintf(ficresvij,"\n");               In version up to 0.92 likelihood was computed
     free_matrix(gp,0,nhstepm,1,nlstate);          as if date of death was unknown. Death was treated as any other
     free_matrix(gm,0,nhstepm,1,nlstate);          health state: the date of the interview describes the actual state
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          and not the date of a change in health state. The former idea was
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          to consider that at each interview the state was recorded
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          (healthy, disable or death) and IMaCh was corrected; but when we
   } /* End age */          introduced the exact date of death then we should have modified
            the contribution of an exact death to the likelihood. This new
   free_vector(xp,1,npar);          contribution is smaller and very dependent of the step unit
   free_matrix(doldm,1,nlstate,1,npar);          stepm. It is no more the probability to die between last interview
   free_matrix(dnewm,1,nlstate,1,nlstate);          and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
 }          probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
 /************ Variance of prevlim ******************/          mortality artificially. The bad side is that we add another loop
 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)          which slows down the processing. The difference can be up to 10%
 {          lower mortality.
   /* Variance of prevalence limit */            */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            lli=log(out[s1][s2] - savm[s1][s2]);
   double **newm;  
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm;          } else if  (s2==-2) {
   int k, cptcode;            for (j=1,survp=0. ; j<=nlstate; j++) 
   double *xp;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   double *gp, *gm;            /*survp += out[s1][j]; */
   double **gradg, **trgradg;            lli= log(survp);
   double age,agelim;          }
   int theta;          
              else if  (s2==-4) { 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");            for (j=3,survp=0. ; j<=nlstate; j++)  
   fprintf(ficresvpl,"# Age");              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   for(i=1; i<=nlstate;i++)            lli= log(survp); 
       fprintf(ficresvpl," %1d-%1d",i,i);          } 
   fprintf(ficresvpl,"\n");  
           else if  (s2==-5) { 
   xp=vector(1,npar);            for (j=1,survp=0. ; j<=2; j++)  
   dnewm=matrix(1,nlstate,1,npar);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   doldm=matrix(1,nlstate,1,nlstate);            lli= log(survp); 
            } 
   hstepm=1*YEARM; /* Every year of age */          
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          else{
   agelim = AGESUP;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            /*  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 */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          } 
     if (stepm >= YEARM) hstepm=1;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          /*if(lli ==000.0)*/
     gradg=matrix(1,npar,1,nlstate);          /*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); */
     gp=vector(1,nlstate);          ipmx +=1;
     gm=vector(1,nlstate);          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(theta=1; theta <=npar; theta++){        } /* end of wave */
       for(i=1; i<=npar; i++){ /* Computes gradient */      } /* end of individual */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }  else if(mle==2){
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(i=1;i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
         gp[i] = prlim[i][i];          for (ii=1;ii<=nlstate+ndeath;ii++)
                for (j=1;j<=nlstate+ndeath;j++){
       for(i=1; i<=npar; i++) /* Computes gradient */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            }
       for(i=1;i<=nlstate;i++)          for(d=0; d<=dh[mi][i]; d++){
         gm[i] = prlim[i][i];            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(i=1;i<=nlstate;i++)            for (kk=1; kk<=cptcovage;kk++) {
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     } /* End theta */            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     trgradg =matrix(1,nlstate,1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     for(j=1; j<=nlstate;j++)            oldm=newm;
       for(theta=1; theta <=npar; theta++)          } /* end mult */
         trgradg[j][theta]=gradg[theta][j];        
           s1=s[mw[mi][i]][i];
     for(i=1;i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
       varpl[i][(int)age] =0.;          bbh=(double)bh[mi][i]/(double)stepm; 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          ipmx +=1;
     for(i=1;i<=nlstate;i++)          sw += weight[i];
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
     fprintf(ficresvpl,"%.0f ",age );      } /* end of individual */
     for(i=1; i<=nlstate;i++)    }  else if(mle==3){  /* exponential inter-extrapolation */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fprintf(ficresvpl,"\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     free_vector(gp,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
     free_vector(gm,1,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
     free_matrix(gradg,1,npar,1,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
     free_matrix(trgradg,1,nlstate,1,npar);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   } /* End age */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   free_vector(xp,1,npar);          for(d=0; d<dh[mi][i]; d++){
   free_matrix(doldm,1,nlstate,1,npar);            newm=savm;
   free_matrix(dnewm,1,nlstate,1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
 /************ Variance of one-step probabilities  ******************/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 {            savm=oldm;
   int i, j, i1, k1, j1, z1;            oldm=newm;
   int k=0, cptcode;          } /* end mult */
   double **dnewm,**doldm;        
   double *xp;          s1=s[mw[mi][i]][i];
   double *gp, *gm;          s2=s[mw[mi+1][i]][i];
   double **gradg, **trgradg;          bbh=(double)bh[mi][i]/(double)stepm; 
   double age,agelim, cov[NCOVMAX];          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 */
   int theta;          ipmx +=1;
   char fileresprob[FILENAMELENGTH];          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   strcpy(fileresprob,"prob");        } /* end of wave */
   strcat(fileresprob,fileres);      } /* end of individual */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     printf("Problem with resultfile: %s\n", fileresprob);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");            for (j=1;j<=nlstate+ndeath;j++){
   fprintf(ficresprob,"# Age");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(i=1; i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(j=1; j<=(nlstate+ndeath);j++)            }
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficresprob,"\n");            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
   xp=vector(1,npar);          
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   cov[1]=1;            oldm=newm;
   j=cptcoveff;          } /* end mult */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        
   j1=0;          s1=s[mw[mi][i]][i];
   for(k1=1; k1<=1;k1++){          s2=s[mw[mi+1][i]][i];
     for(i1=1; i1<=ncodemax[k1];i1++){          if( s2 > nlstate){ 
     j1++;            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
     if  (cptcovn>0) {            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       fprintf(ficresprob, "\n#********** Variable ");          }
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          ipmx +=1;
       fprintf(ficresprob, "**********\n#");          sw += weight[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]); */
       for (age=bage; age<=fage; age ++){        } /* end of wave */
         cov[2]=age;      } /* end of individual */
         for (k=1; k<=cptcovn;k++) {    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                  for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          for (ii=1;ii<=nlstate+ndeath;ii++)
         for (k=1; k<=cptcovprod;k++)            for (j=1;j<=nlstate+ndeath;j++){
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                      savm[ii][j]=(ii==j ? 1.0 : 0.0);
         gradg=matrix(1,npar,1,9);            }
         trgradg=matrix(1,9,1,npar);          for(d=0; d<dh[mi][i]; d++){
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            newm=savm;
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                for (kk=1; kk<=cptcovage;kk++) {
         for(theta=1; theta <=npar; theta++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           for(i=1; i<=npar; i++)            }
             xp[i] = x[i] + (i==theta ?delti[theta]:0);          
                      out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                      savm=oldm;
           k=0;            oldm=newm;
           for(i=1; i<= (nlstate+ndeath); i++){          } /* end mult */
             for(j=1; j<=(nlstate+ndeath);j++){        
               k=k+1;          s1=s[mw[mi][i]][i];
               gp[k]=pmmij[i][j];          s2=s[mw[mi+1][i]][i];
             }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }          ipmx +=1;
                    sw += weight[i];
           for(i=1; i<=npar; i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             xp[i] = x[i] - (i==theta ?delti[theta]:0);          /*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 */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      } /* end of individual */
           k=0;    } /* End of if */
           for(i=1; i<=(nlstate+ndeath); i++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
             for(j=1; j<=(nlstate+ndeath);j++){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
               k=k+1;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
               gm[k]=pmmij[i][j];    return -l;
             }  }
           }  
        /*************** log-likelihood *************/
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  double funcone( double *x)
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    {
         }    /* Same as likeli but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
           for(theta=1; theta <=npar; theta++)    double **out;
             trgradg[j][theta]=gradg[theta][j];    double lli; /* Individual log likelihood */
            double llt;
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    int s1, s2;
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    double bbh, survp;
            /*extern weight */
         pmij(pmmij,cov,ncovmodel,x,nlstate);    /* We are differentiating ll according to initial status */
            /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         k=0;    /*for(i=1;i<imx;i++) 
         for(i=1; i<=(nlstate+ndeath); i++){      printf(" %d\n",s[4][i]);
           for(j=1; j<=(nlstate+ndeath);j++){    */
             k=k+1;    cov[1]=1.;
             gm[k]=pmmij[i][j];  
           }    for(k=1; k<=nlstate; k++) ll[k]=0.;
         }  
          for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      /*printf("\n%d ",(int)age);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      for(mi=1; mi<= wav[i]-1; mi++){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        for (ii=1;ii<=nlstate+ndeath;ii++)
      }*/          for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficresprob,"\n%d ",(int)age);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)        for(d=0; d<dh[mi][i]; d++){
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));          newm=savm;
            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }          for (kk=1; kk<=cptcovage;kk++) {
     }            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
   free_vector(xp,1,npar);          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
   fclose(ficresprob);          savm=oldm;
            oldm=newm;
 }        } /* end mult */
         
 /******************* Printing html file ***********/        s1=s[mw[mi][i]][i];
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \        s2=s[mw[mi+1][i]][i];
  int lastpass, int stepm, int weightopt, char model[],\        bbh=(double)bh[mi][i]/(double)stepm; 
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \        /* bias is positive if real duration
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\         * is higher than the multiple of stepm and negative otherwise.
  char version[], int popforecast, int estepm ){         */
   int jj1, k1, i1, cpt;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   FILE *fichtm;          lli=log(out[s1][s2] - savm[s1][s2]);
   /*char optionfilehtm[FILENAMELENGTH];*/        } else if  (s2==-2) {
           for (j=1,survp=0. ; j<=nlstate; j++) 
   strcpy(optionfilehtm,optionfile);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   strcat(optionfilehtm,".htm");          lli= log(survp);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        }else if (mle==1){
     printf("Problem with %s \n",optionfilehtm), exit(0);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   }        } else if(mle==2){
           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 */
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n        } else if(mle==3){  /* exponential inter-extrapolation */
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n          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 */
 \n        } else if (mle==4){  /* mle=4 no inter-extrapolation */
 Total number of observations=%d <br>\n          lli=log(out[s1][s2]); /* Original formula */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n        } else{  /* mle=0 back to 1 */
 <hr  size=\"2\" color=\"#EC5E5E\">          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
  <ul><li>Outputs files<br>\n          /*lli=log(out[s1][s2]); */ /* Original formula */
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        } /* End of if */
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n        ipmx +=1;
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        sw += weight[i];
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);        if(globpr){
           fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
  fprintf(fichtm,"\n   %11.6f %11.6f %11.6f ", \
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n            llt +=ll[k]*gipmx/gsw;
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
  if(popforecast==1) fprintf(fichtm,"\n          fprintf(ficresilk," %10.6f\n", -llt);
  - 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      } /* end of wave */
         <br>",fileres,fileres,fileres,fileres);    } /* end of individual */
  else    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 fprintf(fichtm," <li>Graphs</li><p>");    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 */
  m=cptcoveff;      gipmx=ipmx;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      gsw=sw;
     }
  jj1=0;    return -l;
  for(k1=1; k1<=m;k1++){  }
    for(i1=1; i1<=ncodemax[k1];i1++){  
        jj1++;  
        if (cptcovn > 0) {  /*************** function likelione ***********/
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
          for (cpt=1; cpt<=cptcoveff;cpt++)  {
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    /* This routine should help understanding what is done with 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");       the selection of individuals/waves and
        }       to check the exact contribution to the likelihood.
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>       Plotting could be done.
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);         */
        for(cpt=1; cpt<nlstate;cpt++){    int k;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    if(*globpri !=0){ /* Just counts and sums, no printings */
        }      strcpy(fileresilk,"ilk"); 
     for(cpt=1; cpt<=nlstate;cpt++) {      strcat(fileresilk,fileres);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
 interval) in state (%d): v%s%d%d.gif <br>        printf("Problem with resultfile: %s\n", fileresilk);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
      }      }
      for(cpt=1; cpt<=nlstate;cpt++) {      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      /*  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(fichtm,"\n<br>- Total life expectancy by age and        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
 health expectancies in states (1) and (2): e%s%d.gif<br>      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    }
 fprintf(fichtm,"\n</body>");  
    }    *fretone=(*funcone)(p);
    }    if(*globpri !=0){
 fclose(fichtm);      fclose(ficresilk);
 }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
 /******************* Gnuplot file **************/    } 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    return;
   }
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;  
   
   strcpy(optionfilegnuplot,optionfilefiname);  /*********** Maximum Likelihood Estimation ***************/
   strcat(optionfilegnuplot,".gp.txt");  
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     printf("Problem with file %s",optionfilegnuplot);  {
   }    int i,j, iter;
     double **xi;
 #ifdef windows    double fret;
     fprintf(ficgp,"cd \"%s\" \n",pathc);    double fretone; /* Only one call to likelihood */
 #endif    /*  char filerespow[FILENAMELENGTH];*/
 m=pow(2,cptcoveff);  
    #ifdef NLOPT
  /* 1eme*/    int creturn;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    nlopt_opt opt;
    for (k1=1; k1<= m ; k1 ++) {    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     double *lb;
 #ifdef windows    double minf; /* the minimum objective value, upon return */
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    double * p1; /* Shifted parameters from 0 instead of 1 */
 #endif    myfunc_data dinst, *d = &dinst;
 #ifdef unix  #endif
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);  
 #endif  
     xi=matrix(1,npar,1,npar);
 for (i=1; i<= nlstate ; i ++) {    for (i=1;i<=npar;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for (j=1;j<=npar;j++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");        xi[i][j]=(i==j ? 1.0 : 0.0);
 }    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    strcpy(filerespow,"pow"); 
     for (i=1; i<= nlstate ; i ++) {    strcat(filerespow,fileres);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");      printf("Problem with resultfile: %s\n", filerespow);
 }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    }
      for (i=1; i<= nlstate ; i ++) {    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    for (i=1;i<=nlstate;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(j=1;j<=nlstate+ndeath;j++)
 }          if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    fprintf(ficrespow,"\n");
 #ifdef unix  #ifdef POWELL
 fprintf(ficgp,"\nset ter gif small size 400,300");    powell(p,xi,npar,ftol,&iter,&fret,func);
 #endif  #endif
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
    }  #ifdef NLOPT
   }  #ifdef NEWUOA
   /*2 eme*/    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   #else
   for (k1=1; k1<= m ; k1 ++) {    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);  #endif
        lb=vector(0,npar-1);
     for (i=1; i<= nlstate+1 ; i ++) {    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
       k=2*i;    nlopt_set_lower_bounds(opt, lb);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    nlopt_set_initial_step1(opt, 0.1);
       for (j=1; j<= nlstate+1 ; j ++) {    
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    d->function = func;
 }      printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    nlopt_set_min_objective(opt, myfunc, d);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    nlopt_set_xtol_rel(opt, ftol);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
       for (j=1; j<= nlstate+1 ; j ++) {      printf("nlopt failed! %d\n",creturn); 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
         else fprintf(ficgp," \%%*lf (\%%*lf)");    else {
 }        printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
       fprintf(ficgp,"\" t\"\" w l 0,");      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      iter=1; /* not equal */
       for (j=1; j<= nlstate+1 ; j ++) {    }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    nlopt_destroy(opt);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  #endif
 }      free_matrix(xi,1,npar,1,npar);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    fclose(ficrespow);
       else fprintf(ficgp,"\" t\"\" w l 0,");    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     }    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   }  
    }
   /*3eme*/  
   /**** Computes Hessian and covariance matrix ***/
   for (k1=1; k1<= m ; k1 ++) {  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     for (cpt=1; cpt<= nlstate ; cpt ++) {  {
       k=2+nlstate*(2*cpt-2);    double  **a,**y,*x,pd;
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    double **hess;
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    int i, j;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    int *indx;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
 */    double gompertz(double p[]);
       for (i=1; i< nlstate ; i ++) {    hess=matrix(1,npar,1,npar);
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);  
     printf("\nCalculation of the hessian matrix. Wait...\n");
       }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    for (i=1;i<=npar;i++){
     }      printf("%d",i);fflush(stdout);
     }      fprintf(ficlog,"%d",i);fflush(ficlog);
       
   /* CV preval stat */       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     for (k1=1; k1<= m ; k1 ++) {      
     for (cpt=1; cpt<nlstate ; cpt ++) {      /*  printf(" %f ",p[i]);
       k=3;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    }
     
       for (i=1; i< nlstate ; i ++)    for (i=1;i<=npar;i++) {
         fprintf(ficgp,"+$%d",k+i+1);      for (j=1;j<=npar;j++)  {
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        if (j>i) { 
                printf(".%d%d",i,j);fflush(stdout);
       l=3+(nlstate+ndeath)*cpt;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          hess[i][j]=hessij(p,delti,i,j,func,npar);
       for (i=1; i< nlstate ; i ++) {          
         l=3+(nlstate+ndeath)*cpt;          hess[j][i]=hess[i][j];    
         fprintf(ficgp,"+$%d",l+i+1);          /*printf(" %lf ",hess[i][j]);*/
       }        }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        }
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    }
     }    printf("\n");
   }      fprintf(ficlog,"\n");
    
   /* proba elementaires */    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
    for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     for(k=1; k <=(nlstate+ndeath); k++){    
       if (k != i) {    a=matrix(1,npar,1,npar);
         for(j=1; j <=ncovmodel; j++){    y=matrix(1,npar,1,npar);
            x=vector(1,npar);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    indx=ivector(1,npar);
           jk++;    for (i=1;i<=npar;i++)
           fprintf(ficgp,"\n");      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         }    ludcmp(a,npar,indx,&pd);
       }  
     }    for (j=1;j<=npar;j++) {
     }      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
     for(jk=1; jk <=m; jk++) {      lubksb(a,npar,indx,x);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);      for (i=1;i<=npar;i++){ 
    i=1;        matcov[i][j]=x[i];
    for(k2=1; k2<=nlstate; k2++) {      }
      k3=i;    }
      for(k=1; k<=(nlstate+ndeath); k++) {  
        if (k != k2){    printf("\n#Hessian matrix#\n");
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    fprintf(ficlog,"\n#Hessian matrix#\n");
 ij=1;    for (i=1;i<=npar;i++) { 
         for(j=3; j <=ncovmodel; j++) {      for (j=1;j<=npar;j++) { 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        printf("%.3e ",hess[i][j]);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        fprintf(ficlog,"%.3e ",hess[i][j]);
             ij++;      }
           }      printf("\n");
           else      fprintf(ficlog,"\n");
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    }
         }  
           fprintf(ficgp,")/(1");    /* Recompute Inverse */
            for (i=1;i<=npar;i++)
         for(k1=1; k1 <=nlstate; k1++){        for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    ludcmp(a,npar,indx,&pd);
 ij=1;  
           for(j=3; j <=ncovmodel; j++){    /*  printf("\n#Hessian matrix recomputed#\n");
           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]]]);    for (j=1;j<=npar;j++) {
             ij++;      for (i=1;i<=npar;i++) x[i]=0;
           }      x[j]=1;
           else      lubksb(a,npar,indx,x);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      for (i=1;i<=npar;i++){ 
           }        y[i][j]=x[i];
           fprintf(ficgp,")");        printf("%.3e ",y[i][j]);
         }        fprintf(ficlog,"%.3e ",y[i][j]);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      printf("\n");
         i=i+ncovmodel;      fprintf(ficlog,"\n");
        }    }
      }    */
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    free_matrix(a,1,npar,1,npar);
    }    free_matrix(y,1,npar,1,npar);
        free_vector(x,1,npar);
   fclose(ficgp);    free_ivector(indx,1,npar);
 }  /* end gnuplot */    free_matrix(hess,1,npar,1,npar);
   
   
 /*************** Moving average **************/  }
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){  
   /*************** hessian matrix ****************/
   int i, cpt, cptcod;  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)  {
       for (i=1; i<=nlstate;i++)    int i;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    int l=1, lmax=20;
           mobaverage[(int)agedeb][i][cptcod]=0.;    double k1,k2;
        double p2[MAXPARM+1]; /* identical to x */
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    double res;
       for (i=1; i<=nlstate;i++){    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    double fx;
           for (cpt=0;cpt<=4;cpt++){    int k=0,kmax=10;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    double l1;
           }  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    fx=func(x);
         }    for (i=1;i<=npar;i++) p2[i]=x[i];
       }    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
     }      l1=pow(10,l);
          delts=delt;
 }      for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
 /************** Forecasting ******************/        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){        p2[theta]=x[theta]-delt;
          k2=func(p2)-fx;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        /*res= (k1-2.0*fx+k2)/delt/delt; */
   int *popage;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        
   double *popeffectif,*popcount;  #ifdef DEBUGHESS
   double ***p3mat;        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);
   char fileresf[FILENAMELENGTH];        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
  agelim=AGESUP;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        }
          else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
            k=kmax; l=lmax*10;
   strcpy(fileresf,"f");        }
   strcat(fileresf,fileres);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   if((ficresf=fopen(fileresf,"w"))==NULL) {          delts=delt;
     printf("Problem with forecast resultfile: %s\n", fileresf);        }
   }      }
   printf("Computing forecasting: result on file '%s' \n", fileresf);    }
     delti[theta]=delts;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    return res; 
     
   if (mobilav==1) {  }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     movingaverage(agedeb, fage, ageminpar, mobaverage);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   }  {
     int i;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int l=1, lmax=20;
   if (stepm<=12) stepsize=1;    double k1,k2,k3,k4,res,fx;
      double p2[MAXPARM+1];
   agelim=AGESUP;    int k;
    
   hstepm=1;    fx=func(x);
   hstepm=hstepm/stepm;    for (k=1; k<=2; k++) {
   yp1=modf(dateintmean,&yp);      for (i=1;i<=npar;i++) p2[i]=x[i];
   anprojmean=yp;      p2[thetai]=x[thetai]+delti[thetai]/k;
   yp2=modf((yp1*12),&yp);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   mprojmean=yp;      k1=func(p2)-fx;
   yp1=modf((yp2*30.5),&yp);    
   jprojmean=yp;      p2[thetai]=x[thetai]+delti[thetai]/k;
   if(jprojmean==0) jprojmean=1;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   if(mprojmean==0) jprojmean=1;      k2=func(p2)-fx;
      
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      p2[thetai]=x[thetai]-delti[thetai]/k;
        p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   for(cptcov=1;cptcov<=i2;cptcov++){      k3=func(p2)-fx;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    
       k=k+1;      p2[thetai]=x[thetai]-delti[thetai]/k;
       fprintf(ficresf,"\n#******");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(j=1;j<=cptcoveff;j++) {      k4=func(p2)-fx;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       }  #ifdef DEBUG
       fprintf(ficresf,"******\n");      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       fprintf(ficresf,"# StartingAge FinalAge");      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  #endif
          }
          return res;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  }
         fprintf(ficresf,"\n");  
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  { 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    int i,imax,j,k; 
           nhstepm = nhstepm/hstepm;    double big,dum,sum,temp; 
              double *vv; 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   
           oldm=oldms;savm=savms;    vv=vector(1,n); 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      *d=1.0; 
            for (i=1;i<=n;i++) { 
           for (h=0; h<=nhstepm; h++){      big=0.0; 
             if (h==(int) (calagedate+YEARM*cpt)) {      for (j=1;j<=n;j++) 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);        if ((temp=fabs(a[i][j])) > big) big=temp; 
             }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
             for(j=1; j<=nlstate+ndeath;j++) {      vv[i]=1.0/big; 
               kk1=0.;kk2=0;    } 
               for(i=1; i<=nlstate;i++) {                  for (j=1;j<=n;j++) { 
                 if (mobilav==1)      for (i=1;i<j;i++) { 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        sum=a[i][j]; 
                 else {        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        a[i][j]=sum; 
                 }      } 
                      big=0.0; 
               }      for (i=j;i<=n;i++) { 
               if (h==(int)(calagedate+12*cpt)){        sum=a[i][j]; 
                 fprintf(ficresf," %.3f", kk1);        for (k=1;k<j;k++) 
                                  sum -= a[i][k]*a[k][j]; 
               }        a[i][j]=sum; 
             }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           }          big=dum; 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          imax=i; 
         }        } 
       }      } 
     }      if (j != imax) { 
   }        for (k=1;k<=n;k++) { 
                  dum=a[imax][k]; 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
   fclose(ficresf);        } 
 }        *d = -(*d); 
 /************** Forecasting ******************/        vv[imax]=vv[j]; 
 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){      } 
        indx[j]=imax; 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      if (a[j][j] == 0.0) a[j][j]=TINY; 
   int *popage;      if (j != n) { 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        dum=1.0/(a[j][j]); 
   double *popeffectif,*popcount;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   double ***p3mat,***tabpop,***tabpopprev;      } 
   char filerespop[FILENAMELENGTH];    } 
     free_vector(vv,1,n);  /* Doesn't work */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  ;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  } 
   agelim=AGESUP;  
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  void lubksb(double **a, int n, int *indx, double b[]) 
    { 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    int i,ii=0,ip,j; 
      double sum; 
     
   strcpy(filerespop,"pop");    for (i=1;i<=n;i++) { 
   strcat(filerespop,fileres);      ip=indx[i]; 
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      sum=b[ip]; 
     printf("Problem with forecast resultfile: %s\n", filerespop);      b[ip]=b[i]; 
   }      if (ii) 
   printf("Computing forecasting: result on file '%s' \n", filerespop);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      b[i]=sum; 
     } 
   if (mobilav==1) {    for (i=n;i>=1;i--) { 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      sum=b[i]; 
     movingaverage(agedeb, fage, ageminpar, mobaverage);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   }      b[i]=sum/a[i][i]; 
     } 
   stepsize=(int) (stepm+YEARM-1)/YEARM;  } 
   if (stepm<=12) stepsize=1;  
    void pstamp(FILE *fichier)
   agelim=AGESUP;  {
      fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   hstepm=1;  }
   hstepm=hstepm/stepm;  
    /************ Frequencies ********************/
   if (popforecast==1) {  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
     if((ficpop=fopen(popfile,"r"))==NULL) {  {  /* Some frequencies */
       printf("Problem with population file : %s\n",popfile);exit(0);    
     }    int i, m, jk, j1, bool, z1,j;
     popage=ivector(0,AGESUP);    int first;
     popeffectif=vector(0,AGESUP);    double ***freq; /* Frequencies */
     popcount=vector(0,AGESUP);    double *pp, **prop;
        double pos,posprop, k2, dateintsum=0,k2cpt=0;
     i=1;      char fileresp[FILENAMELENGTH];
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    
        pp=vector(1,nlstate);
     imx=i;    prop=matrix(1,nlstate,iagemin,iagemax+3);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    strcpy(fileresp,"p");
   }    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
   for(cptcov=1;cptcov<=i2;cptcov++){      printf("Problem with prevalence resultfile: %s\n", fileresp);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       k=k+1;      exit(0);
       fprintf(ficrespop,"\n#******");    }
       for(j=1;j<=cptcoveff;j++) {    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    j1=0;
       }    
       fprintf(ficrespop,"******\n");    j=cptcoveff;
       fprintf(ficrespop,"# Age");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  
       if (popforecast==1)  fprintf(ficrespop," [Population]");    first=1;
        
       for (cpt=0; cpt<=0;cpt++) {    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
            /*    j1++;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
           nhstepm = nhstepm/hstepm;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                    scanf("%d", i);*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (i=-5; i<=nlstate+ndeath; i++)  
           oldm=oldms;savm=savms;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for(m=iagemin; m <= iagemax+3; m++)
                      freq[i][jk][m]=0;
           for (h=0; h<=nhstepm; h++){        
             if (h==(int) (calagedate+YEARM*cpt)) {        for (i=1; i<=nlstate; i++)  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          for(m=iagemin; m <= iagemax+3; m++)
             }            prop[i][m]=0;
             for(j=1; j<=nlstate+ndeath;j++) {        
               kk1=0.;kk2=0;        dateintsum=0;
               for(i=1; i<=nlstate;i++) {                      k2cpt=0;
                 if (mobilav==1)        for (i=1; i<=imx; i++) {
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          bool=1;
                 else {          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            for (z1=1; z1<=cptcoveff; z1++)       
                 }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
               }                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
               if (h==(int)(calagedate+12*cpt)){                bool=0;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;                /* 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(ficrespop," %.3f", kk1);                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
               }                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
             }              } 
             for(i=1; i<=nlstate;i++){          }
               kk1=0.;   
                 for(j=1; j<=nlstate;j++){          if (bool==1){
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];            for(m=firstpass; m<=lastpass; m++){
                 }              k2=anint[m][i]+(mint[m][i]/12.);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
             }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);                if (m<lastpass) {
           }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         }                }
       }                
                  if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   /******/                  dateintsum=dateintsum+k2;
                   k2cpt++;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {                }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                  /*}*/
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){            }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          }
           nhstepm = nhstepm/hstepm;        } /* end i */
                   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
           oldm=oldms;savm=savms;        pstamp(ficresp);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          if  (cptcovn>0) {
           for (h=0; h<=nhstepm; h++){          fprintf(ficresp, "\n#********** Variable "); 
             if (h==(int) (calagedate+YEARM*cpt)) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          fprintf(ficresp, "**********\n#");
             }          fprintf(ficlog, "\n#********** Variable "); 
             for(j=1; j<=nlstate+ndeath;j++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
               kk1=0.;kk2=0;          fprintf(ficlog, "**********\n#");
               for(i=1; i<=nlstate;i++) {                      }
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            for(i=1; i<=nlstate;i++) 
               }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        fprintf(ficresp, "\n");
             }        
           }        for(i=iagemin; i <= iagemax+3; i++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if(i==iagemax+3){
         }            fprintf(ficlog,"Total");
       }          }else{
    }            if(first==1){
   }              first=0;
                printf("See log file for details...\n");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
             fprintf(ficlog,"Age %d", i);
   if (popforecast==1) {          }
     free_ivector(popage,0,AGESUP);          for(jk=1; jk <=nlstate ; jk++){
     free_vector(popeffectif,0,AGESUP);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     free_vector(popcount,0,AGESUP);              pp[jk] += freq[jk][m][i]; 
   }          }
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(jk=1; jk <=nlstate ; jk++){
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(m=-1, pos=0; m <=0 ; m++)
   fclose(ficrespop);              pos += freq[jk][m][i];
 }            if(pp[jk]>=1.e-10){
               if(first==1){
 /***********************************************/                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 /**************** Main Program *****************/              }
 /***********************************************/              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
 int main(int argc, char *argv[])              if(first==1)
 {                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;            }
   double agedeb, agefin,hf;          }
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  
           for(jk=1; jk <=nlstate ; jk++){
   double fret;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   double **xi,tmp,delta;              pp[jk] += freq[jk][m][i];
           }       
   double dum; /* Dummy variable */          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   double ***p3mat;            pos += pp[jk];
   int *indx;            posprop += prop[jk][i];
   char line[MAXLINE], linepar[MAXLINE];          }
   char title[MAXLINE];          for(jk=1; jk <=nlstate ; jk++){
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];            if(pos>=1.e-5){
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];              if(first==1)
                  printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
   char filerest[FILENAMELENGTH];              if(first==1)
   char fileregp[FILENAMELENGTH];                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   char popfile[FILENAMELENGTH];              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];            }
   int firstobs=1, lastobs=10;            if( i <= iagemax){
   int sdeb, sfin; /* Status at beginning and end */              if(pos>=1.e-5){
   int c,  h , cpt,l;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   int ju,jl, mi;                /*probs[i][jk][j1]= pp[jk]/pos;*/
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;              }
   int mobilav=0,popforecast=0;              else
   int hstepm, nhstepm;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;            }
           }
   double bage, fage, age, agelim, agebase;          
   double ftolpl=FTOL;          for(jk=-1; jk <=nlstate+ndeath; jk++)
   double **prlim;            for(m=-1; m <=nlstate+ndeath; m++)
   double *severity;              if(freq[jk][m][i] !=0 ) {
   double ***param; /* Matrix of parameters */              if(first==1)
   double  *p;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   double **matcov; /* Matrix of covariance */                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   double ***delti3; /* Scale */              }
   double *delti; /* Scale */          if(i <= iagemax)
   double ***eij, ***vareij;            fprintf(ficresp,"\n");
   double **varpl; /* Variances of prevalence limits by age */          if(first==1)
   double *epj, vepp;            printf("Others in log...\n");
   double kk1, kk2;          fprintf(ficlog,"\n");
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        }
          /*}*/
     }
   char version[80]="Imach version 0.8a, May 2002, INED-EUROREVES ";    dateintmean=dateintsum/k2cpt; 
   char *alph[]={"a","a","b","c","d","e"}, str[4];   
     fclose(ficresp);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   char z[1]="c", occ;    free_vector(pp,1,nlstate);
 #include <sys/time.h>    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
 #include <time.h>    /* End of Freq */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  }
    
   /* long total_usecs;  /************ Prevalence ********************/
   struct timeval start_time, end_time;  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)
    {  
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   getcwd(pathcd, size);       in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
   printf("\n%s",version);    */
   if(argc <=1){   
     printf("\nEnter the parameter file name: ");    int i, m, jk, j1, bool, z1,j;
     scanf("%s",pathtot);  
   }    double **prop;
   else{    double posprop; 
     strcpy(pathtot,argv[1]);    double  y2; /* in fractional years */
   }    int iagemin, iagemax;
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    int first; /** to stop verbosity which is redirected to log file */
   /*cygwin_split_path(pathtot,path,optionfile);  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    iagemin= (int) agemin;
   /* cutv(path,optionfile,pathtot,'\\');*/    iagemax= (int) agemax;
     /*pp=vector(1,nlstate);*/
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   chdir(path);    j1=0;
   replace(pathc,path);    
     /*j=cptcoveff;*/
 /*-------- arguments in the command line --------*/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
   strcpy(fileres,"r");    first=1;
   strcat(fileres, optionfilefiname);    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
   strcat(fileres,".txt");    /* Other files have txt extension */      /*for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;*/
   /*---------arguments file --------*/        
         for (i=1; i<=nlstate; i++)  
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          for(m=iagemin; m <= iagemax+3; m++)
     printf("Problem with optionfile %s\n",optionfile);            prop[i][m]=0.0;
     goto end;       
   }        for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
   strcpy(filereso,"o");          if  (cptcovn>0) {
   strcat(filereso,fileres);            for (z1=1; z1<=cptcoveff; z1++) 
   if((ficparo=fopen(filereso,"w"))==NULL) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;                bool=0;
   }          } 
           if (bool==1) { 
   /* Reads comments: lines beginning with '#' */            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   while((c=getc(ficpar))=='#' && c!= EOF){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     ungetc(c,ficpar);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     fgets(line, MAXLINE, ficpar);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     puts(line);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     fputs(line,ficparo);                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) { 
   ungetc(c,ficpar);                  /*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];
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);                  prop[s[m][i]][iagemax+3] += weight[i]; 
   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);              }
 while((c=getc(ficpar))=='#' && c!= EOF){            } /* end selection of waves */
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        for(i=iagemin; i <= iagemax+3; i++){  
     fputs(line,ficparo);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   }            posprop += prop[jk][i]; 
   ungetc(c,ficpar);          } 
            
              for(jk=1; jk <=nlstate ; jk++){     
   covar=matrix(0,NCOVMAX,1,n);            if( i <=  iagemax){ 
   cptcovn=0;              if(posprop>=1.e-5){ 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                probs[i][jk][j1]= prop[jk][i]/posprop;
               } else{
   ncovmodel=2+cptcovn;                if(first==1){
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                  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]);
   /* Read guess parameters */                }
   /* Reads comments: lines beginning with '#' */              }
   while((c=getc(ficpar))=='#' && c!= EOF){            } 
     ungetc(c,ficpar);          }/* end jk */ 
     fgets(line, MAXLINE, ficpar);        }/* end i */ 
     puts(line);      /*} *//* end i1 */
     fputs(line,ficparo);    } /* end j1 */
   }    
   ungetc(c,ficpar);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
      /*free_vector(pp,1,nlstate);*/
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     for(i=1; i <=nlstate; i++)  }  /* End of prevalence */
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);  /************* Waves Concatenation ***************/
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);  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)
       for(k=1; k<=ncovmodel;k++){  {
         fscanf(ficpar," %lf",&param[i][j][k]);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         printf(" %lf",param[i][j][k]);       Death is a valid wave (if date is known).
         fprintf(ficparo," %lf",param[i][j][k]);       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]
       fscanf(ficpar,"\n");       and mw[mi+1][i]. dh depends on stepm.
       printf("\n");       */
       fprintf(ficparo,"\n");  
     }    int i, mi, m;
      /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;       double sum=0., jmean=0.;*/
     int first;
   p=param[1][1];    int j, k=0,jk, ju, jl;
      double sum=0.;
   /* Reads comments: lines beginning with '#' */    first=0;
   while((c=getc(ficpar))=='#' && c!= EOF){    jmin=100000;
     ungetc(c,ficpar);    jmax=-1;
     fgets(line, MAXLINE, ficpar);    jmean=0.;
     puts(line);    for(i=1; i<=imx; i++){
     fputs(line,ficparo);      mi=0;
   }      m=firstpass;
   ungetc(c,ficpar);      while(s[m][i] <= nlstate){
         if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          mw[++mi][i]=m;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        if(m >=lastpass)
   for(i=1; i <=nlstate; i++){          break;
     for(j=1; j <=nlstate+ndeath-1; j++){        else
       fscanf(ficpar,"%1d%1d",&i1,&j1);          m++;
       printf("%1d%1d",i,j);      }/* end while */
       fprintf(ficparo,"%1d%1d",i1,j1);      if (s[m][i] > nlstate){
       for(k=1; k<=ncovmodel;k++){        mi++;     /* Death is another wave */
         fscanf(ficpar,"%le",&delti3[i][j][k]);        /* if(mi==0)  never been interviewed correctly before death */
         printf(" %le",delti3[i][j][k]);           /* Only death is a correct wave */
         fprintf(ficparo," %le",delti3[i][j][k]);        mw[mi][i]=m;
       }      }
       fscanf(ficpar,"\n");  
       printf("\n");      wav[i]=mi;
       fprintf(ficparo,"\n");      if(mi==0){
     }        nbwarn++;
   }        if(first==0){
   delti=delti3[1][1];          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
            first=1;
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){        if(first==1){
     ungetc(c,ficpar);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     fgets(line, MAXLINE, ficpar);        }
     puts(line);      } /* end mi==0 */
     fputs(line,ficparo);    } /* End individuals */
   }  
   ungetc(c,ficpar);    for(i=1; i<=imx; i++){
        for(mi=1; mi<wav[i];mi++){
   matcov=matrix(1,npar,1,npar);        if (stepm <=0)
   for(i=1; i <=npar; i++){          dh[mi][i]=1;
     fscanf(ficpar,"%s",&str);        else{
     printf("%s",str);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     fprintf(ficparo,"%s",str);            if (agedc[i] < 2*AGESUP) {
     for(j=1; j <=i; j++){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       fscanf(ficpar," %le",&matcov[i][j]);              if(j==0) j=1;  /* Survives at least one month after exam */
       printf(" %.5le",matcov[i][j]);              else if(j<0){
       fprintf(ficparo," %.5le",matcov[i][j]);                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]);
     fscanf(ficpar,"\n");                j=1; /* Temporary Dangerous patch */
     printf("\n");                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(ficparo,"\n");                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);
   for(i=1; i <=npar; i++)              }
     for(j=i+1;j<=npar;j++)              k=k+1;
       matcov[i][j]=matcov[j][i];              if (j >= jmax){
                    jmax=j;
   printf("\n");                ijmax=i;
               }
               if (j <= jmin){
     /*-------- Rewriting paramater file ----------*/                jmin=j;
      strcpy(rfileres,"r");    /* "Rparameterfile */                ijmin=i;
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/              }
      strcat(rfileres,".");    /* */              sum=sum+j;
      strcat(rfileres,optionfilext);    /* Other files have txt extension */              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     if((ficres =fopen(rfileres,"w"))==NULL) {              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       printf("Problem writing new parameter file: %s\n", fileres);goto end;            }
     }          }
     fprintf(ficres,"#%s\n",version);          else{
                j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     /*-------- data file ----------*/  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;            k=k+1;
     }            if (j >= jmax) {
               jmax=j;
     n= lastobs;              ijmax=i;
     severity = vector(1,maxwav);            }
     outcome=imatrix(1,maxwav+1,1,n);            else if (j <= jmin){
     num=ivector(1,n);              jmin=j;
     moisnais=vector(1,n);              ijmin=i;
     annais=vector(1,n);            }
     moisdc=vector(1,n);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     andc=vector(1,n);            /*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]);*/
     agedc=vector(1,n);            if(j<0){
     cod=ivector(1,n);              nberr++;
     weight=vector(1,n);              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]);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */              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]);
     mint=matrix(1,maxwav,1,n);            }
     anint=matrix(1,maxwav,1,n);            sum=sum+j;
     s=imatrix(1,maxwav+1,1,n);          }
     adl=imatrix(1,maxwav+1,1,n);              jk= j/stepm;
     tab=ivector(1,NCOVMAX);          jl= j -jk*stepm;
     ncodemax=ivector(1,8);          ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     i=1;            if(jl==0){
     while (fgets(line, MAXLINE, fic) != NULL)    {              dh[mi][i]=jk;
       if ((i >= firstobs) && (i <=lastobs)) {              bh[mi][i]=0;
                    }else{ /* We want a negative bias in order to only have interpolation ie
         for (j=maxwav;j>=1;j--){                    * to avoid the price of an extra matrix product in likelihood */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);              dh[mi][i]=jk+1;
           strcpy(line,stra);              bh[mi][i]=ju;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            }
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          }else{
         }            if(jl <= -ju){
                      dh[mi][i]=jk;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=jl;       /* bias is positive if real duration
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                                   * is higher than the multiple of stepm and negative otherwise.
                                    */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            else{
               dh[mi][i]=jk+1;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=ju;
         for (j=ncovcol;j>=1;j--){            }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            if(dh[mi][i]==0){
         }              dh[mi][i]=1; /* At least one step */
         num[i]=atol(stra);              bh[mi][i]=ju; /* At least one step */
                      /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
         /*if((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;}*/          } /* end if mle */
         }
         i=i+1;      } /* end wave */
       }    }
     }    jmean=sum/k;
     /* printf("ii=%d", ij);    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);
        scanf("%d",i);*/    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
   imx=i-1; /* Number of individuals */   }
   
   /* for (i=1; i<=imx; i++){  /*********** Tricode ****************************/
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
     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;    /**< 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 
    /*  for (i=1; i<=imx; i++){    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
      if (s[4][i]==9)  s[4][i]=-1;     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
      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]));}*/    /* nbcode[Tvar[j]][1]= 
      */
    
   /* Calculation of the number of parameter from char model*/    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   Tvar=ivector(1,15);    int modmaxcovj=0; /* Modality max of covariates j */
   Tprod=ivector(1,15);    int cptcode=0; /* Modality max of covariates j */
   Tvaraff=ivector(1,15);    int modmincovj=0; /* Modality min of covariates j */
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);        
        cptcoveff=0; 
   if (strlen(model) >1){   
     j=0, j1=0, k1=1, k2=1;    for (k=-1; k < maxncov; k++) Ndum[k]=0;
     j=nbocc(model,'+');    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
     j1=nbocc(model,'*');  
     cptcovn=j+1;    /* Loop on covariates without age and products */
     cptcovprod=j1;    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 
     strcpy(modelsav,model);                                 modality of this covariate Vj*/ 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
       printf("Error. Non available option model=%s ",model);                                      * If product of Vn*Vm, still boolean *:
       goto end;                                      * 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
     for(i=(j+1); i>=1;i--){                                        modality of the nth covariate of individual i. */
       cutv(stra,strb,modelsav,'+');        if (ij > modmaxcovj)
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);          modmaxcovj=ij; 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        else if (ij < modmincovj) 
       /*scanf("%d",i);*/          modmincovj=ij; 
       if (strchr(strb,'*')) {        if ((ij < -1) && (ij > NCOVMAX)){
         cutv(strd,strc,strb,'*');          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
         if (strcmp(strc,"age")==0) {          exit(1);
           cptcovprod--;        }else
           cutv(strb,stre,strd,'V');        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
           Tvar[i]=atoi(stre);        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
           cptcovage++;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
             Tage[cptcovage]=i;        /* getting the maximum value of the modality of the covariate
             /*printf("stre=%s ", stre);*/           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
         }           female is 1, then modmaxcovj=1.*/
         else if (strcmp(strd,"age")==0) {      }
           cptcovprod--;      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
           cutv(strb,stre,strc,'V');      cptcode=modmaxcovj;
           Tvar[i]=atoi(stre);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
           cptcovage++;     /*for (i=0; i<=cptcode; i++) {*/
           Tage[cptcovage]=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]);
         else {        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           cutv(strb,stre,strc,'V');          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
           Tvar[i]=ncovcol+k1;        }
           cutv(strb,strc,strd,'V');        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
           Tprod[k1]=i;           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
           Tvard[k1][1]=atoi(strc);      } /* Ndum[-1] number of undefined modalities */
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
           for (k=1; k<=lastobs;k++)      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];         modmincovj=3; modmaxcovj = 7;
           k1++;         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
           k2=k2+2;         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;
       else {         nbcode[Tvar[j]][1]=0;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/         nbcode[Tvar[j]][2]=1;
        /*  scanf("%d",i);*/         nbcode[Tvar[j]][3]=2;
       cutv(strd,strc,strb,'V');      */
       Tvar[i]=atoi(strc);      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 */
       strcpy(modelsav,stra);          for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          /*recode from 0 */
         scanf("%d",i);*/          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; */
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);            ij++;
   printf("cptcovprod=%d ", cptcovprod);          }
   scanf("%d ",i);*/          if (ij > ncodemax[j]) break; 
     fclose(fic);        }  /* end of loop on */
       } /* end of loop on modality */ 
     /*  if(mle==1){*/    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     if (weightopt != 1) { /* Maximisation without weights*/    
       for(i=1;i<=n;i++) weight[i]=1.0;   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     }    
     /*-calculation of age at interview from date of interview and age at death -*/    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
     agev=matrix(1,maxwav,1,imx);     /* 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 */ 
     for (i=1; i<=imx; i++) {     Ndum[ij]++; 
       for(m=2; (m<= maxwav); m++) {   } 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  
          anint[m][i]=9999;   ij=1;
          s[m][i]=-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(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;     if((Ndum[i]!=0) && (i<=ncovcol)){
       }       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
     }       Tvaraff[ij]=i; /*For printing (unclear) */
        ij++;
     for (i=1; i<=imx; i++)  {     }else
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);         Tvaraff[ij]=0;
       for(m=1; (m<= maxwav); m++){   }
         if(s[m][i] >0){   ij--;
           if (s[m][i] >= nlstate+1) {   cptcoveff=ij; /*Number of total covariates*/
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)  }
                 agev[m][i]=agedc[i];  
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  
            else {  /*********** Health Expectancies ****************/
               if (andc[i]!=9999){  
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
               agev[m][i]=-1;  
               }  {
             }    /* Health expectancies, no variances */
           }    int i, j, nhstepm, hstepm, h, nstepm;
           else if(s[m][i] !=9){ /* Should no more exist */    int nhstepma, nstepma; /* Decreasing with age */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    double age, agelim, hf;
             if(mint[m][i]==99 || anint[m][i]==9999)    double ***p3mat;
               agev[m][i]=1;    double eip;
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];    pstamp(ficreseij);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    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");
             else if(agev[m][i] >agemax){    for(i=1; i<=nlstate;i++){
               agemax=agev[m][i];      for(j=1; j<=nlstate;j++){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        fprintf(ficreseij," e%1d%1d ",i,j);
             }      }
             /*agev[m][i]=anint[m][i]-annais[i];*/      fprintf(ficreseij," e%1d. ",i);
             /*   agev[m][i] = age[i]+2*m;*/    }
           }    fprintf(ficreseij,"\n");
           else { /* =9 */  
             agev[m][i]=1;    
             s[m][i]=-1;    if(estepm < stepm){
           }      printf ("Problem %d lower than %d\n",estepm, stepm);
         }    }
         else /*= 0 Unknown */    else  hstepm=estepm;   
           agev[m][i]=1;    /* 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 
     for (i=1; i<=imx; i++)  {     * progression in between and thus overestimating or underestimating according
       for(m=1; (m<= maxwav); m++){     * to the curvature of the survival function. If, for the same date, we 
         if (s[m][i] > (nlstate+ndeath)) {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           printf("Error: Wrong value in nlstate or ndeath\n");       * to compare the new estimate of Life expectancy with the same linear 
           goto end;     * 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. 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
     free_vector(severity,1,maxwav);       Look at hpijx to understand the reason of that which relies in memory size
     free_imatrix(outcome,1,maxwav+1,1,n);       and note for a fixed period like estepm months */
     free_vector(moisnais,1,n);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     free_vector(annais,1,n);       survival function given by stepm (the optimization length). Unfortunately it
     /* free_matrix(mint,1,maxwav,1,n);       means that if the survival funtion is printed only each two years of age and if
        free_matrix(anint,1,maxwav,1,n);*/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     free_vector(moisdc,1,n);       results. So we changed our mind and took the option of the best precision.
     free_vector(andc,1,n);    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      
     wav=ivector(1,imx);    agelim=AGESUP;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    /* If stepm=6 months */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
             in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     /* Concatenates waves */      
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  /* 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 */ 
       Tcode=ivector(1,100);    /* if (stepm >= YEARM) hstepm=1;*/
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       ncodemax[1]=1;    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
          for (age=bage; age<=fage; age ++){ 
    codtab=imatrix(1,100,1,10);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
    h=0;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
    m=pow(2,cptcoveff);      /* if (stepm >= YEARM) hstepm=1;*/
        nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){      /* If stepm=6 months */
        for(j=1; j <= ncodemax[k]; j++){      /* Computed by stepm unit matrices, product of hstepma matrices, stored
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
            h++;      
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/      
          }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        }      
      }      printf("%d|",(int)age);fflush(stdout);
    }      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);      
       codtab[1][2]=1;codtab[2][2]=2; */      /* Computing expectancies */
    /* for(i=1; i <=m ;i++){      for(i=1; i<=nlstate;i++)
       for(k=1; k <=cptcovn; k++){        for(j=1; j<=nlstate;j++)
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);          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;
       printf("\n");            
       }            /* 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]);*/
       scanf("%d",i);*/  
              }
    /* Calculates basic frequencies. Computes observed prevalence at single age  
        and prints on file fileres'p'. */      fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
            eip=0;
            for(j=1; j<=nlstate;j++){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          eip +=eij[i][j][(int)age];
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficreseij,"%9.4f", eip );
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      }
            fprintf(ficreseij,"\n");
     /* 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) */    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     if(mle==1){    fprintf(ficlog,"\n");
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    
     }  }
      
     /*--------- results files --------------*/  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[] )
     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);  
    {
     /* Covariances of health expectancies eij and of total life expectancies according
    jk=1;     to initial status i, ei. .
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    */
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
    for(i=1,jk=1; i <=nlstate; i++){    int nhstepma, nstepma; /* Decreasing with age */
      for(k=1; k <=(nlstate+ndeath); k++){    double age, agelim, hf;
        if (k != i)    double ***p3matp, ***p3matm, ***varhe;
          {    double **dnewm,**doldm;
            printf("%d%d ",i,k);    double *xp, *xm;
            fprintf(ficres,"%1d%1d ",i,k);    double **gp, **gm;
            for(j=1; j <=ncovmodel; j++){    double ***gradg, ***trgradg;
              printf("%f ",p[jk]);    int theta;
              fprintf(ficres,"%f ",p[jk]);  
              jk++;    double eip, vip;
            }  
            printf("\n");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
            fprintf(ficres,"\n");    xp=vector(1,npar);
          }    xm=vector(1,npar);
      }    dnewm=matrix(1,nlstate*nlstate,1,npar);
    }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
  if(mle==1){    
     /* Computing hessian and covariance matrix */    pstamp(ficresstdeij);
     ftolhess=ftol; /* Usually correct */    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     hesscov(matcov, p, npar, delti, ftolhess, func);    fprintf(ficresstdeij,"# Age");
  }    for(i=1; i<=nlstate;i++){
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      for(j=1; j<=nlstate;j++)
     printf("# Scales (for hessian or gradient estimation)\n");        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
      for(i=1,jk=1; i <=nlstate; i++){      fprintf(ficresstdeij," e%1d. ",i);
       for(j=1; j <=nlstate+ndeath; j++){    }
         if (j!=i) {    fprintf(ficresstdeij,"\n");
           fprintf(ficres,"%1d%1d",i,j);  
           printf("%1d%1d",i,j);    pstamp(ficrescveij);
           for(k=1; k<=ncovmodel;k++){    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
             printf(" %.5e",delti[jk]);    fprintf(ficrescveij,"# Age");
             fprintf(ficres," %.5e",delti[jk]);    for(i=1; i<=nlstate;i++)
             jk++;      for(j=1; j<=nlstate;j++){
           }        cptj= (j-1)*nlstate+i;
           printf("\n");        for(i2=1; i2<=nlstate;i2++)
           fprintf(ficres,"\n");          for(j2=1; j2<=nlstate;j2++){
         }            cptj2= (j2-1)*nlstate+i2;
       }            if(cptj2 <= cptj)
      }              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
              }
     k=1;      }
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    fprintf(ficrescveij,"\n");
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    
     for(i=1;i<=npar;i++){    if(estepm < stepm){
       /*  if (k>nlstate) k=1;      printf ("Problem %d lower than %d\n",estepm, stepm);
       i1=(i-1)/(ncovmodel*nlstate)+1;    }
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    else  hstepm=estepm;   
       printf("%s%d%d",alph[k],i1,tab[i]);*/    /* We compute the life expectancy from trapezoids spaced every estepm months
       fprintf(ficres,"%3d",i);     * This is mainly to measure the difference between two models: for example
       printf("%3d",i);     * if stepm=24 months pijx are given only every 2 years and by summing them
       for(j=1; j<=i;j++){     * we are calculating an estimate of the Life Expectancy assuming a linear 
         fprintf(ficres," %.5e",matcov[i][j]);     * progression in between and thus overestimating or underestimating according
         printf(" %.5e",matcov[i][j]);     * 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
       fprintf(ficres,"\n");     * to compare the new estimate of Life expectancy with the same linear 
       printf("\n");     * hypothesis. A more precise result, taking into account a more precise
       k++;     * curvature will be obtained if estepm is as small as stepm. */
     }  
        /* For example we decided to compute the life expectancy with the smallest unit */
     while((c=getc(ficpar))=='#' && c!= EOF){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       ungetc(c,ficpar);       nhstepm is the number of hstepm from age to agelim 
       fgets(line, MAXLINE, ficpar);       nstepm is the number of stepm from age to agelin. 
       puts(line);       Look at hpijx to understand the reason of that which relies in memory size
       fputs(line,ficparo);       and note for a fixed period like estepm months */
     }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     ungetc(c,ficpar);       survival function given by stepm (the optimization length). Unfortunately it
     estepm=0;       means that if the survival funtion is printed only each two years of age and if
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     if (estepm==0 || estepm < stepm) estepm=stepm;       results. So we changed our mind and took the option of the best precision.
     if (fage <= 2) {    */
       bage = ageminpar;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       fage = agemaxpar;  
     }    /* If stepm=6 months */
        /* nhstepm age range expressed in number of stepm */
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    agelim=AGESUP;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      /* if (stepm >= YEARM) hstepm=1;*/
     while((c=getc(ficpar))=='#' && c!= EOF){    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     puts(line);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fputs(line,ficparo);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   }    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   ungetc(c,ficpar);    gp=matrix(0,nhstepm,1,nlstate*nlstate);
      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);  
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    for (age=bage; age<=fage; age ++){ 
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
            /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   while((c=getc(ficpar))=='#' && c!= EOF){      /* if (stepm >= YEARM) hstepm=1;*/
     ungetc(c,ficpar);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     fgets(line, MAXLINE, ficpar);  
     puts(line);      /* If stepm=6 months */
     fputs(line,ficparo);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   }         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   ungetc(c,ficpar);      
        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      /* Computing  Variances of health expectancies */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
   fscanf(ficpar,"pop_based=%d\n",&popbased);      for(theta=1; theta <=npar; theta++){
   fprintf(ficparo,"pop_based=%d\n",popbased);          for(i=1; i<=npar; i++){ 
   fprintf(ficres,"pop_based=%d\n",popbased);            xp[i] = x[i] + (i==theta ?delti[theta]:0);
            xm[i] = x[i] - (i==theta ?delti[theta]:0);
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
     fgets(line, MAXLINE, ficpar);        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     puts(line);    
     fputs(line,ficparo);        for(j=1; j<= nlstate; j++){
   }          for(i=1; i<=nlstate; i++){
   ungetc(c,ficpar);            for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);            }
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          }
         }
        
 while((c=getc(ficpar))=='#' && c!= EOF){        for(ij=1; ij<= nlstate*nlstate; ij++)
     ungetc(c,ficpar);          for(h=0; h<=nhstepm-1; h++){
     fgets(line, MAXLINE, ficpar);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
     puts(line);          }
     fputs(line,ficparo);      }/* End theta */
   }      
   ungetc(c,ficpar);      
       for(h=0; h<=nhstepm-1; h++)
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);        for(j=1; j<=nlstate*nlstate;j++)
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          for(theta=1; theta <=npar; theta++)
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            trgradg[h][j][theta]=gradg[h][theta][j];
       
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
        for(ij=1;ij<=nlstate*nlstate;ij++)
 /*------------ gnuplot -------------*/        for(ji=1;ji<=nlstate*nlstate;ji++)
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);          varhe[ij][ji][(int)age] =0.;
    
 /*------------ free_vector  -------------*/       printf("%d|",(int)age);fflush(stdout);
  chdir(path);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         for(h=0;h<=nhstepm-1;h++){
  free_ivector(wav,1,imx);        for(k=0;k<=nhstepm-1;k++){
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
  free_ivector(num,1,n);          for(ij=1;ij<=nlstate*nlstate;ij++)
  free_vector(agedc,1,n);            for(ji=1;ji<=nlstate*nlstate;ji++)
  /*free_matrix(covar,1,NCOVMAX,1,n);*/              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
  fclose(ficparo);        }
  fclose(ficres);      }
   
 /*--------- index.htm --------*/      /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);      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++){
   /*--------------- Prevalence limit --------------*/            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
              
   strcpy(filerespl,"pl");            /* 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]);*/
   strcat(filerespl,fileres);  
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }      fprintf(ficresstdeij,"%3.0f",age );
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      for(i=1; i<=nlstate;i++){
   fprintf(ficrespl,"#Prevalence limit\n");        eip=0.;
   fprintf(ficrespl,"#Age ");        vip=0.;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        for(j=1; j<=nlstate;j++){
   fprintf(ficrespl,"\n");          eip += eij[i][j][(int)age];
            for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   prlim=matrix(1,nlstate,1,nlstate);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      fprintf(ficresstdeij,"\n");
   k=0;  
   agebase=ageminpar;      fprintf(ficrescveij,"%3.0f",age );
   agelim=agemaxpar;      for(i=1; i<=nlstate;i++)
   ftolpl=1.e-10;        for(j=1; j<=nlstate;j++){
   i1=cptcoveff;          cptj= (j-1)*nlstate+i;
   if (cptcovn < 1){i1=1;}          for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
   for(cptcov=1;cptcov<=i1;cptcov++){              cptj2= (j2-1)*nlstate+i2;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              if(cptj2 <= cptj)
         k=k+1;                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
         /*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++)      fprintf(ficrescveij,"\n");
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     
         fprintf(ficrespl,"******\n");    }
            free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
         for (age=agebase; age<=agelim; age++){    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
           fprintf(ficrespl,"%.0f",age );    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
           for(i=1; i<=nlstate;i++)    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespl," %.5f", prlim[i][i]);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespl,"\n");    printf("\n");
         }    fprintf(ficlog,"\n");
       }  
     }    free_vector(xm,1,npar);
   fclose(ficrespl);    free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   /*------------- h Pij x at various ages ------------*/    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
      free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  /************ 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[])
   printf("Computing pij: result on file '%s' \n", filerespij);  {
      /* Variance of health expectancies */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   /*if (stepm<=24) stepsize=2;*/    /* double **newm;*/
     double **dnewm,**doldm;
   agelim=AGESUP;    double **dnewmp,**doldmp;
   hstepm=stepsize*YEARM; /* Every year of age */    int i, j, nhstepm, hstepm, h, nstepm ;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    int k;
      double *xp;
   k=0;    double **gp, **gm;  /* for var eij */
   for(cptcov=1;cptcov<=i1;cptcov++){    double ***gradg, ***trgradg; /*for var eij */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double **gradgp, **trgradgp; /* for var p point j */
       k=k+1;    double *gpp, *gmp; /* for var p point j */
         fprintf(ficrespij,"\n#****** ");    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
         for(j=1;j<=cptcoveff;j++)    double ***p3mat;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double age,agelim, hf;
         fprintf(ficrespij,"******\n");    double ***mobaverage;
            int theta;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    char digit[4];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    char digitp[25];
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    char fileresprobmorprev[FILENAMELENGTH];
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      if(popbased==1){
           fprintf(ficrespij,"# Age");      if(mobilav!=0)
           for(i=1; i<=nlstate;i++)        strcpy(digitp,"-populbased-mobilav-");
             for(j=1; j<=nlstate+ndeath;j++)      else strcpy(digitp,"-populbased-nomobil-");
               fprintf(ficrespij," %1d-%1d",i,j);    }
           fprintf(ficrespij,"\n");    else 
            for (h=0; h<=nhstepm; h++){      strcpy(digitp,"-stablbased-");
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)    if (mobilav!=0) {
               for(j=1; j<=nlstate+ndeath;j++)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
             fprintf(ficrespij,"\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
              }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
           fprintf(ficrespij,"\n");    }
         }  
     }    strcpy(fileresprobmorprev,"prmorprev"); 
   }    sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   fclose(ficrespij);    strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
   /*---------- Forecasting ------------------*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   if((stepm == 1) && (strcmp(model,".")==0)){    }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);   
   }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   else{    pstamp(ficresprobmorprev);
     erreur=108;    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);
     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(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++)
   /*---------- Health expectancies and variances ------------*/        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
   strcpy(filerest,"t");    fprintf(ficresprobmorprev,"\n");
   strcat(filerest,fileres);    fprintf(ficgp,"\n# Routine varevsij");
   if((ficrest=fopen(filerest,"w"))==NULL) {    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    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);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
   strcpy(filerese,"e");    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
   strcat(filerese,fileres);    if(popbased==1)
   if((ficreseij=fopen(filerese,"w"))==NULL) {      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);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    else
   }      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
  strcpy(fileresv,"v");      for(j=1; j<=nlstate;j++)
   strcat(fileresv,fileres);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    fprintf(ficresvij,"\n");
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }    xp=vector(1,npar);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    dnewm=matrix(1,nlstate,1,npar);
   calagedate=-1;    doldm=matrix(1,nlstate,1,nlstate);
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    gpp=vector(nlstate+1,nlstate+ndeath);
       k=k+1;    gmp=vector(nlstate+1,nlstate+ndeath);
       fprintf(ficrest,"\n#****** ");    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       for(j=1;j<=cptcoveff;j++)    
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if(estepm < stepm){
       fprintf(ficrest,"******\n");      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
       fprintf(ficreseij,"\n#****** ");    else  hstepm=estepm;   
       for(j=1;j<=cptcoveff;j++)    /* For example we decided to compute the life expectancy with the smallest unit */
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       fprintf(ficreseij,"******\n");       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
       fprintf(ficresvij,"\n#****** ");       Look at function hpijx to understand why (it is linked to memory size questions) */
       for(j=1;j<=cptcoveff;j++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       survival function given by stepm (the optimization length). Unfortunately it
       fprintf(ficresvij,"******\n");       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 
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       results. So we changed our mind and took the option of the best precision.
       oldm=oldms;savm=savms;    */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      agelim = AGESUP;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       oldm=oldms;savm=savms;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);      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);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      gm=matrix(0,nhstepm,1,nlstate);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");  
       for(theta=1; theta <=npar; theta++){
       epj=vector(1,nlstate+1);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       for(age=bage; age <=fage ;age++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        }
         if (popbased==1) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           for(i=1; i<=nlstate;i++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             prlim[i][i]=probs[(int)age][i][k];  
         }        if (popbased==1) {
                  if(mobilav ==0){
         fprintf(ficrest," %4.0f",age);            for(i=1; i<=nlstate;i++)
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){              prlim[i][i]=probs[(int)age][i][ij];
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          }else{ /* mobilav */ 
             epj[j] += prlim[i][i]*eij[i][j][(int)age];            for(i=1; i<=nlstate;i++)
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/              prlim[i][i]=mobaverage[(int)age][i][ij];
           }          }
           epj[nlstate+1] +=epj[j];        }
         }    
         for(j=1; j<= nlstate; j++){
         for(i=1, vepp=0.;i <=nlstate;i++)          for(h=0; h<=nhstepm; h++){
           for(j=1;j <=nlstate;j++)            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
             vepp += vareij[i][j][(int)age];              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
         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]));        /* This for computing probability of death (h=1 means
         }           computed over hstepm matrices product = hstepm*stepm months) 
         fprintf(ficrest,"\n");           as a weighted average of prlim.
       }        */
     }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
 free_matrix(mint,1,maxwav,1,n);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);        }    
     free_vector(weight,1,n);        /* end probability of death */
   fclose(ficreseij);  
   fclose(ficresvij);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   fclose(ficrest);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   fclose(ficpar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   free_vector(epj,1,nlstate+1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     
   /*------- Variance limit prevalence------*/          if (popbased==1) {
           if(mobilav ==0){
   strcpy(fileresvpl,"vpl");            for(i=1; i<=nlstate;i++)
   strcat(fileresvpl,fileres);              prlim[i][i]=probs[(int)age][i][ij];
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          }else{ /* mobilav */ 
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);            for(i=1; i<=nlstate;i++)
     exit(0);              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        }
   
   k=0;        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
   for(cptcov=1;cptcov<=i1;cptcov++){          for(h=0; h<=nhstepm; h++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       k=k+1;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       fprintf(ficresvpl,"\n#****** ");          }
       for(j=1;j<=cptcoveff;j++)        }
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        /* This for computing probability of death (h=1 means
       fprintf(ficresvpl,"******\n");           computed over hstepm matrices product = hstepm*stepm months) 
                 as a weighted average of prlim.
       varpl=matrix(1,nlstate,(int) bage, (int) fage);        */
       oldm=oldms;savm=savms;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
  }        }    
         /* end probability of death */
   fclose(ficresvpl);  
         for(j=1; j<= nlstate; j++) /* vareij */
   /*---------- End : free ----------------*/          for(h=0; h<=nhstepm; h++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
            gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
          }
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      } /* End theta */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
    
   free_matrix(matcov,1,npar,1,npar);      for(h=0; h<=nhstepm; h++) /* veij */
   free_vector(delti,1,npar);        for(j=1; j<=nlstate;j++)
   free_matrix(agev,1,maxwav,1,imx);          for(theta=1; theta <=npar; theta++)
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);            trgradg[h][j][theta]=gradg[h][theta][j];
   
   if(erreur >0)      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     printf("End of Imach with error or warning %d\n",erreur);        for(theta=1; theta <=npar; theta++)
   else   printf("End of Imach\n");          trgradgp[j][theta]=gradgp[theta][j];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    
    
   /* 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);*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   /*printf("Total time was %d uSec.\n", total_usecs);*/      for(i=1;i<=nlstate;i++)
   /*------ End -----------*/        for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
  end:      for(h=0;h<=nhstepm;h++){
 #ifdef windows        for(k=0;k<=nhstepm;k++){
   /* chdir(pathcd);*/          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
 #endif          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
  /*system("wgnuplot graph.plt");*/          for(i=1;i<=nlstate;i++)
  /*system("../gp37mgw/wgnuplot graph.plt");*/            for(j=1;j<=nlstate;j++)
  /*system("cd ../gp37mgw");*/              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        }
  strcpy(plotcmd,GNUPLOTPROGRAM);      }
  strcat(plotcmd," ");    
  strcat(plotcmd,optionfilegnuplot);      /* pptj */
  system(plotcmd);      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);
 #ifdef windows      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   while (z[0] != 'q') {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     /* chdir(path); */          varppt[j][i]=doldmp[j][i];
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");      /* end ppptj */
     scanf("%s",z);      /*  x centered again */
     if (z[0] == 'c') system("./imach");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     else if (z[0] == 'e') system(optionfilehtm);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     else if (z[0] == 'g') system(plotcmd);   
     else if (z[0] == 'q') exit(0);      if (popbased==1) {
   }        if(mobilav ==0){
 #endif          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 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.1.41  
changed lines
  Added in v.1.164


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