Diff for /imach/src/imach.c between versions 1.49 and 1.169

version 1.49, 2002/06/20 14:03:39 version 1.169, 2014/12/22 23:08:31
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.169  2014/12/22 23:08:31  brouard
      Summary: 0.98p
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Outputs some informations on compiler used, OS etc. Testing on different platforms.
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.168  2014/12/22 15:17:42  brouard
   case of a health survey which is our main interest) -2- at least a    Summary: udate
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.167  2014/12/22 13:50:56  brouard
   computed from the time spent in each health state according to a    Summary: Testing uname and compiler version and if compiled 32 or 64
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Testing on Linux 64
   simplest model is the multinomial logistic model where pij is the  
   probability to be observed in state j at the second wave    Revision 1.166  2014/12/22 11:40:47  brouard
   conditional to be observed in state i at the first wave. Therefore    *** empty log message ***
   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 1.165  2014/12/16 11:20:36  brouard
   complex model than "constant and age", you should modify the program    Summary: After compiling on Visual C
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    * imach.c (Module): Merging 1.61 to 1.162
   convergence.  
     Revision 1.164  2014/12/16 10:52:11  brouard
   The advantage of this computer programme, compared to a simple    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    * imach.c (Module): Merging 1.61 to 1.162
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.163  2014/12/16 10:30:11  brouard
     * imach.c (Module): Merging 1.61 to 1.162
   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 1.162  2014/09/25 11:43:39  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    Summary: temporary backup 0.99!
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.1  2014/09/16 11:06:58  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    Summary: With some code (wrong) for nlopt
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Author:
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.161  2014/09/15 20:41:41  brouard
   of the life expectancies. It also computes the prevalence limits.    Summary: Problem with macro SQR on Intel compiler
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.160  2014/09/02 09:24:05  brouard
            Institut national d'études démographiques, Paris.    *** empty log message ***
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.159  2014/09/01 10:34:10  brouard
   It is copyrighted identically to a GNU software product, ie programme and    Summary: WIN32
   software can be distributed freely for non commercial use. Latest version    Author: Brouard
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.158  2014/08/27 17:11:51  brouard
      *** empty log message ***
 #include <math.h>  
 #include <stdio.h>    Revision 1.157  2014/08/27 16:26:55  brouard
 #include <stdlib.h>    Summary: Preparing windows Visual studio version
 #include <unistd.h>    Author: Brouard
   
 #define MAXLINE 256    In order to compile on Visual studio, time.h is now correct and time_t
 #define GNUPLOTPROGRAM "gnuplot"    and tm struct should be used. difftime should be used but sometimes I
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    just make the differences in raw time format (time(&now).
 #define FILENAMELENGTH 80    Trying to suppress #ifdef LINUX
 /*#define DEBUG*/    Add xdg-open for __linux in order to open default browser.
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.156  2014/08/25 20:10:10  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    *** empty log message ***
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.155  2014/08/25 18:32:34  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Summary: New compile, minor changes
     Author: Brouard
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.154  2014/06/20 17:32:08  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Summary: Outputs now all graphs of convergence to period prevalence
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.153  2014/06/20 16:45:46  brouard
 #define YEARM 12. /* Number of months per year */    Summary: If 3 live state, convergence to period prevalence on same graph
 #define AGESUP 130    Author: Brouard
 #define AGEBASE 40  
 #ifdef windows    Revision 1.152  2014/06/18 17:54:09  brouard
 #define DIRSEPARATOR '\\'    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 #else  
 #define DIRSEPARATOR '/'    Revision 1.151  2014/06/18 16:43:30  brouard
 #endif    *** empty log message ***
   
 char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";    Revision 1.150  2014/06/18 16:42:35  brouard
 int erreur; /* Error number */    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 int nvar;    Author: brouard
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.149  2014/06/18 15:51:14  brouard
 int nlstate=2; /* Number of live states */    Summary: Some fixes in parameter files errors
 int ndeath=1; /* Number of dead states */    Author: Nicolas Brouard
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.148  2014/06/17 17:38:48  brouard
     Summary: Nothing new
 int *wav; /* Number of waves for this individuual 0 is possible */    Author: Brouard
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Just a new packaging for OS/X version 0.98nS
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.147  2014/06/16 10:33:11  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    *** empty log message ***
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.146  2014/06/16 10:20:28  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Summary: Merge
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Author: Brouard
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *fichtm; /* Html File */    Merge, before building revised version.
 FILE *ficreseij;  
 char filerese[FILENAMELENGTH];    Revision 1.145  2014/06/10 21:23:15  brouard
 FILE  *ficresvij;    Summary: Debugging with valgrind
 char fileresv[FILENAMELENGTH];    Author: Nicolas Brouard
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];    Lot of changes in order to output the results with some covariates
 char title[MAXLINE];    After the Edimburgh REVES conference 2014, it seems mandatory to
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    improve the code.
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    No more memory valgrind error but a lot has to be done in order to
     continue the work of splitting the code into subroutines.
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    Also, decodemodel has been improved. Tricode is still not
     optimal. nbcode should be improved. Documentation has been added in
 char filerest[FILENAMELENGTH];    the source code.
 char fileregp[FILENAMELENGTH];  
 char popfile[FILENAMELENGTH];    Revision 1.143  2014/01/26 09:45:38  brouard
     Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define NR_END 1    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    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 NRANSI  
 #define ITMAX 200    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   
 #define TOL 2.0e-4    Revision 1.141  2014/01/26 02:42:01  brouard
     * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.140  2011/09/02 10:37:54  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Summary: times.h is ok with mingw32 now.
   
 #define GOLD 1.618034    Revision 1.139  2010/06/14 07:50:17  brouard
 #define GLIMIT 100.0    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 #define TINY 1.0e-20    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   
 static double maxarg1,maxarg2;    Revision 1.138  2010/04/30 18:19:40  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    *** empty log message ***
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.137  2010/04/29 18:11:38  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Module): Checking covariates for more complex models
 #define rint(a) floor(a+0.5)    than V1+V2. A lot of change to be done. Unstable.
   
 static double sqrarg;    Revision 1.136  2010/04/26 20:30:53  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (Module): merging some libgsl code. Fixing computation
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    of likelione (using inter/intrapolation if mle = 0) in order to
     get same likelihood as if mle=1.
 int imx;    Some cleaning of code and comments added.
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    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 estepm;  
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Revision 1.134  2009/10/29 13:18:53  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.133  2009/07/06 10:21:25  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    just nforces
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    Revision 1.132  2009/07/06 08:22:05  brouard
     Many tings
 double *weight;  
 int **s; /* Status */    Revision 1.131  2009/06/20 16:22:47  brouard
 double *agedc, **covar, idx;    Some dimensions resccaled
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.130  2009/05/26 06:44:34  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): Max Covariate is now set to 20 instead of 8. A
 double ftolhess; /* Tolerance for computing hessian */    lot of cleaning with variables initialized to 0. Trying to make
     V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.129  2007/08/31 13:49:27  lievre
 {    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.128  2006/06/30 13:02:05  brouard
     (Module): Clarifications on computing e.j
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.127  2006/04/28 18:11:50  brouard
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */    (Module): Yes the sum of survivors was wrong since
    if ( s == NULL ) {                   /* no directory, so use current */    imach-114 because nhstepm was no more computed in the age
 #if     defined(__bsd__)                /* get current working directory */    loop. Now we define nhstepma in the age loop.
       extern char       *getwd( );    (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
       if ( getwd( dirc ) == NULL ) {    and then all the health expectancies with variances or standard
 #else    deviation (needs data from the Hessian matrices) which slows the
       extern char       *getcwd( );    computation.
     In the future we should be able to stop the program is only health
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    expectancies and graph are needed without standard deviations.
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.126  2006/04/28 17:23:28  brouard
       }    (Module): Yes the sum of survivors was wrong since
       strcpy( name, path );             /* we've got it */    imach-114 because nhstepm was no more computed in the age
    } else {                             /* strip direcotry from path */    loop. Now we define nhstepma in the age loop.
       s++;                              /* after this, the filename */    Version 0.98h
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.125  2006/04/04 15:20:31  lievre
       strcpy( name, s );                /* save file name */    Errors in calculation of health expectancies. Age was not initialized.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Forecasting file added.
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.124  2006/03/22 17:13:53  lievre
    l1 = strlen( dirc );                 /* length of directory */    Parameters are printed with %lf instead of %f (more numbers after the comma).
 #ifdef windows    The log-likelihood is printed in the log file
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Revision 1.123  2006/03/20 10:52:43  brouard
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    * imach.c (Module): <title> changed, corresponds to .htm file
 #endif    name. <head> headers where missing.
    s = strrchr( name, '.' );            /* find last / */  
    s++;    * imach.c (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 1.122  2006/03/20 09:45:41  brouard
     (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 /******************************************/    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 void replace(char *s, char*t)    1.
 {    Version 0.98g
   int i;  
   int lg=20;    Revision 1.121  2006/03/16 17:45:01  lievre
   i=0;    * imach.c (Module): Comments concerning covariates added
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    * imach.c (Module): refinements in the computation of lli if
     (s[i] = t[i]);    status=-2 in order to have more reliable computation if stepm is
     if (t[i]== '\\') s[i]='/';    not 1 month. Version 0.98f
   }  
 }    Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
 int nbocc(char *s, char occ)    status=-2 in order to have more reliable computation if stepm is
 {    not 1 month. Version 0.98f
   int i,j=0;  
   int lg=20;    Revision 1.119  2006/03/15 17:42:26  brouard
   i=0;    (Module): Bug if status = -2, the loglikelihood was
   lg=strlen(s);    computed as likelihood omitting the logarithm. Version O.98e
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;    Revision 1.118  2006/03/14 18:20:07  brouard
   }    (Module): varevsij Comments added explaining the second
   return j;    table of variances if popbased=1 .
 }    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
 void cutv(char *u,char *v, char*t, char occ)    (Module): Version 0.98d
 {  
   int i,lg,j,p=0;    Revision 1.117  2006/03/14 17:16:22  brouard
   i=0;    (Module): varevsij Comments added explaining the second
   for(j=0; j<=strlen(t)-1; j++) {    table of variances if popbased=1 .
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   }    (Module): Function pstamp added
     (Module): Version 0.98d
   lg=strlen(t);  
   for(j=0; j<p; j++) {    Revision 1.116  2006/03/06 10:29:27  brouard
     (u[j] = t[j]);    (Module): Variance-covariance wrong links and
   }    varian-covariance of ej. is needed (Saito).
      u[p]='\0';  
     Revision 1.115  2006/02/27 12:17:45  brouard
    for(j=0; j<= lg; j++) {    (Module): One freematrix added in mlikeli! 0.98c
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.114  2006/02/26 12:57:58  brouard
 }    (Module): Some improvements in processing parameter
     filename with strsep.
 /********************** nrerror ********************/  
     Revision 1.113  2006/02/24 14:20:24  brouard
 void nrerror(char error_text[])    (Module): Memory leaks checks with valgrind and:
 {    datafile was not closed, some imatrix were not freed and on matrix
   fprintf(stderr,"ERREUR ...\n");    allocation too.
   fprintf(stderr,"%s\n",error_text);  
   exit(1);    Revision 1.112  2006/01/30 09:55:26  brouard
 }    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 /*********************** vector *******************/  
 double *vector(int nl, int nh)    Revision 1.111  2006/01/25 20:38:18  brouard
 {    (Module): Lots of cleaning and bugs added (Gompertz)
   double *v;    (Module): Comments can be added in data file. Missing date values
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    can be a simple dot '.'.
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.110  2006/01/25 00:51:50  brouard
 }    (Module): Lots of cleaning and bugs added (Gompertz)
   
 /************************ free vector ******************/    Revision 1.109  2006/01/24 19:37:15  brouard
 void free_vector(double*v, int nl, int nh)    (Module): Comments (lines starting with a #) are allowed in data.
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.108  2006/01/19 18:05:42  lievre
 }    Gnuplot problem appeared...
     To be fixed
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Revision 1.107  2006/01/19 16:20:37  brouard
 {    Test existence of gnuplot in imach path
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Revision 1.106  2006/01/19 13:24:36  brouard
   if (!v) nrerror("allocation failure in ivector");    Some cleaning and links added in html output
   return v-nl+NR_END;  
 }    Revision 1.105  2006/01/05 20:23:19  lievre
     *** empty log message ***
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)    Revision 1.104  2005/09/30 16:11:43  lievre
 {    (Module): sump fixed, loop imx fixed, and simplifications.
   free((FREE_ARG)(v+nl-NR_END));    (Module): If the status is missing at the last wave but we know
 }    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
 /******************* imatrix *******************************/    contributions to the likelihood is 1 - Prob of dying from last
 int **imatrix(long nrl, long nrh, long ncl, long nch)    health status (= 1-p13= p11+p12 in the easiest case of somebody in
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    the healthy state at last known wave). Version is 0.98
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Revision 1.103  2005/09/30 15:54:49  lievre
   int **m;    (Module): sump fixed, loop imx fixed, and simplifications.
    
   /* allocate pointers to rows */    Revision 1.102  2004/09/15 17:31:30  brouard
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Add the possibility to read data file including tab characters.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.101  2004/09/15 10:38:38  brouard
   m -= nrl;    Fix on curr_time
    
      Revision 1.100  2004/07/12 18:29:06  brouard
   /* allocate rows and set pointers to them */    Add version for Mac OS X. Just define UNIX in Makefile
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.99  2004/06/05 08:57:40  brouard
   m[nrl] += NR_END;    *** empty log message ***
   m[nrl] -= ncl;  
      Revision 1.98  2004/05/16 15:05:56  brouard
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    New version 0.97 . First attempt to estimate force of mortality
      directly from the data i.e. without the need of knowing the health
   /* return pointer to array of pointers to rows */    state at each age, but using a Gompertz model: log u =a + b*age .
   return m;    This is the basic analysis of mortality and should be done before any
 }    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
 /****************** free_imatrix *************************/    from other sources like vital statistic data.
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    The same imach parameter file can be used but the option for mle should be -3.
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Agnès, who wrote this part of the code, tried to keep most of the
 {    former routines in order to include the new code within the former code.
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    The output is very simple: only an estimate of the intercept and of
 }    the slope with 95% confident intervals.
   
 /******************* matrix *******************************/    Current limitations:
 double **matrix(long nrl, long nrh, long ncl, long nch)    A) Even if you enter covariates, i.e. with the
 {    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    B) There is no computation of Life Expectancy nor Life Table.
   double **m;  
     Revision 1.97  2004/02/20 13:25:42  lievre
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Version 0.96d. Population forecasting command line is (temporarily)
   if (!m) nrerror("allocation failure 1 in matrix()");    suppressed.
   m += NR_END;  
   m -= nrl;    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    rewritten within the same printf. Workaround: many printfs.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.95  2003/07/08 07:54:34  brouard
   m[nrl] -= ncl;    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    matrix (cov(a12,c31) instead of numbers.
   return m;  
 }    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    Revision 1.93  2003/06/25 16:33:55  brouard
 {    (Module): On windows (cygwin) function asctime_r doesn't
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    exist so I changed back to asctime which exists.
   free((FREE_ARG)(m+nrl-NR_END));    (Module): Version 0.96b
 }  
     Revision 1.92  2003/06/25 16:30:45  brouard
 /******************* ma3x *******************************/    (Module): On windows (cygwin) function asctime_r doesn't
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    exist so I changed back to asctime which exists.
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    Revision 1.91  2003/06/25 15:30:29  brouard
   double ***m;    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    helps to forecast when convergence will be reached. Elapsed time
   if (!m) nrerror("allocation failure 1 in matrix()");    is stamped in powell.  We created a new html file for the graphs
   m += NR_END;    concerning matrix of covariance. It has extension -cov.htm.
   m -= nrl;  
     Revision 1.90  2003/06/24 12:34:15  brouard
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Module): Some bugs corrected for windows. Also, when
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    mle=-1 a template is output in file "or"mypar.txt with the design
   m[nrl] += NR_END;    of the covariance matrix to be input.
   m[nrl] -= ncl;  
     Revision 1.89  2003/06/24 12:30:52  brouard
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    of the covariance matrix to be input.
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;    Revision 1.88  2003/06/23 17:54:56  brouard
   m[nrl][ncl] -= nll;    * 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.
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;    Revision 1.87  2003/06/18 12:26:01  brouard
      Version 0.96
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    Revision 1.86  2003/06/17 20:04:08  brouard
     for (j=ncl+1; j<=nch; j++)    (Module): Change position of html and gnuplot routines and added
       m[i][j]=m[i][j-1]+nlay;    routine fileappend.
   }  
   return m;    Revision 1.85  2003/06/17 13:12:43  brouard
 }    * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
 /*************************free ma3x ************************/    prior to the death. In this case, dh was negative and likelihood
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    was wrong (infinity). We still send an "Error" but patch by
 {    assuming that the date of death was just one stepm after the
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    interview.
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    (Repository): Because some people have very long ID (first column)
   free((FREE_ARG)(m+nrl-NR_END));    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)
 /***************** f1dim *************************/    (Repository): No more line truncation errors.
 extern int ncom;  
 extern double *pcom,*xicom;    Revision 1.84  2003/06/13 21:44:43  brouard
 extern double (*nrfunc)(double []);    * imach.c (Repository): Replace "freqsummary" at a correct
      place. It differs from routine "prevalence" which may be called
 double f1dim(double x)    many times. Probs is memory consuming and must be used with
 {    parcimony.
   int j;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   double f;  
   double *xt;    Revision 1.83  2003/06/10 13:39:11  lievre
      *** empty log message ***
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    Revision 1.82  2003/06/05 15:57:20  brouard
   f=(*nrfunc)(xt);    Add log in  imach.c and  fullversion number is now printed.
   free_vector(xt,1,ncom);  
   return f;  */
 }  /*
      Interpolated Markov Chain
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    Short summary of the programme:
 {    
   int iter;    This program computes Healthy Life Expectancies from
   double a,b,d,etemp;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   double fu,fv,fw,fx;    first survey ("cross") where individuals from different ages are
   double ftemp;    interviewed on their health status or degree of disability (in the
   double p,q,r,tol1,tol2,u,v,w,x,xm;    case of a health survey which is our main interest) -2- at least a
   double e=0.0;    second wave of interviews ("longitudinal") which measure each change
      (if any) in individual health status.  Health expectancies are
   a=(ax < cx ? ax : cx);    computed from the time spent in each health state according to a
   b=(ax > cx ? ax : cx);    model. More health states you consider, more time is necessary to reach the
   x=w=v=bx;    Maximum Likelihood of the parameters involved in the model.  The
   fw=fv=fx=(*f)(x);    simplest model is the multinomial logistic model where pij is the
   for (iter=1;iter<=ITMAX;iter++) {    probability to be observed in state j at the second wave
     xm=0.5*(a+b);    conditional to be observed in state i at the first wave. Therefore
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    'age' is age and 'sex' is a covariate. If you want to have a more
     printf(".");fflush(stdout);    complex model than "constant and age", you should modify the program
 #ifdef DEBUG    where the markup *Covariates have to be included here again* invites
     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);    you to do it.  More covariates you add, slower the
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    convergence.
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    The advantage of this computer programme, compared to a simple
       *xmin=x;    multinomial logistic model, is clear when the delay between waves is not
       return fx;    identical for each individual. Also, if a individual missed an
     }    intermediate interview, the information is lost, but taken into
     ftemp=fu;    account using an interpolation or extrapolation.  
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);    hPijx is the probability to be observed in state i at age x+h
       q=(x-v)*(fx-fw);    conditional to the observed state i at age x. The delay 'h' can be
       p=(x-v)*q-(x-w)*r;    split into an exact number (nh*stepm) of unobserved intermediate
       q=2.0*(q-r);    states. This elementary transition (by month, quarter,
       if (q > 0.0) p = -p;    semester or year) is modelled as a multinomial logistic.  The hPx
       q=fabs(q);    matrix is simply the matrix product of nh*stepm elementary matrices
       etemp=e;    and the contribution of each individual to the likelihood is simply
       e=d;    hPijx.
       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));    Also this programme outputs the covariance matrix of the parameters but also
       else {    of the life expectancies. It also computes the period (stable) prevalence. 
         d=p/q;    
         u=x+d;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
         if (u-a < tol2 || b-u < tol2)             Institut national d'études démographiques, Paris.
           d=SIGN(tol1,xm-x);    This software have been partly granted by Euro-REVES, a concerted action
       }    from the European Union.
     } else {    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
     }    can be accessed at http://euroreves.ined.fr/imach .
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     if (fu <= fx) {    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
       if (u >= x) a=x; else b=x;    
       SHFT(v,w,x,u)    **********************************************************************/
         SHFT(fv,fw,fx,fu)  /*
         } else {    main
           if (u < x) a=u; else b=u;    read parameterfile
           if (fu <= fw || w == x) {    read datafile
             v=w;    concatwav
             w=u;    freqsummary
             fv=fw;    if (mle >= 1)
             fw=fu;      mlikeli
           } else if (fu <= fv || v == x || v == w) {    print results files
             v=u;    if mle==1 
             fv=fu;       computes hessian
           }    read end of parameter file: agemin, agemax, bage, fage, estepm
         }        begin-prev-date,...
   }    open gnuplot file
   nrerror("Too many iterations in brent");    open html file
   *xmin=x;    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
   return fx;     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
 }                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
       freexexit2 possible for memory heap.
 /****************** mnbrak ***********************/  
     h Pij x                         | pij_nom  ficrestpij
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
             double (*func)(double))         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
 {         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   double ulim,u,r,q, dum;  
   double fu;         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
   *fa=(*func)(*ax);    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   *fb=(*func)(*bx);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   if (*fb > *fa) {     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)    forecasting if prevfcast==1 prevforecast call prevalence()
       }    health expectancies
   *cx=(*bx)+GOLD*(*bx-*ax);    Variance-covariance of DFLE
   *fc=(*func)(*cx);    prevalence()
   while (*fb > *fc) {     movingaverage()
     r=(*bx-*ax)*(*fb-*fc);    varevsij() 
     q=(*bx-*cx)*(*fb-*fa);    if popbased==1 varevsij(,popbased)
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    total life expectancies
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    Variance of period (stable) prevalence
     ulim=(*bx)+GLIMIT*(*cx-*bx);   end
     if ((*bx-u)*(u-*cx) > 0.0) {  */
       fu=(*func)(u);  
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define POWELL /* Instead of NLOPT */
       fu=(*func)(u);  
       if (fu < *fc) {  #include <math.h>
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #include <stdio.h>
           SHFT(*fb,*fc,fu,(*func)(u))  #include <stdlib.h>
           }  #include <string.h>
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  #ifdef _WIN32
       fu=(*func)(u);  #include <io.h>
     } else {  #else
       u=(*cx)+GOLD*(*cx-*bx);  #include <unistd.h>
       fu=(*func)(u);  #endif
     }  
     SHFT(*ax,*bx,*cx,u)  #include <limits.h>
       SHFT(*fa,*fb,*fc,fu)  #include <sys/types.h>
       }  #include <sys/utsname.h>
 }  #include <sys/stat.h>
   #include <errno.h>
 /*************** linmin ************************/  /* extern int errno; */
   
 int ncom;  /* #ifdef LINUX */
 double *pcom,*xicom;  /* #include <time.h> */
 double (*nrfunc)(double []);  /* #include "timeval.h" */
    /* #else */
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  /* #include <sys/time.h> */
 {  /* #endif */
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);  #include <time.h>
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  #ifdef GSL
               double *fc, double (*func)(double));  #include <gsl/gsl_errno.h>
   int j;  #include <gsl/gsl_multimin.h>
   double xx,xmin,bx,ax;  #endif
   double fx,fb,fa;  
    
   ncom=n;  #ifdef NLOPT
   pcom=vector(1,n);  #include <nlopt.h>
   xicom=vector(1,n);  typedef struct {
   nrfunc=func;    double (* function)(double [] );
   for (j=1;j<=n;j++) {  } myfunc_data ;
     pcom[j]=p[j];  #endif
     xicom[j]=xi[j];  
   }  /* #include <libintl.h> */
   ax=0.0;  /* #define _(String) gettext (String) */
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  #define GNUPLOTPROGRAM "gnuplot"
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #endif  #define FILENAMELENGTH 132
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
     p[j] += xi[j];  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   }  
   free_vector(xicom,1,n);  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
   free_vector(pcom,1,n);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
 }  
   #define NINTERVMAX 8
 /*************** powell ************************/  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
             double (*func)(double []))  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
 {  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
   void linmin(double p[], double xi[], int n, double *fret,  #define MAXN 20000
               double (*func)(double []));  #define YEARM 12. /**< Number of months per year */
   int i,ibig,j;  #define AGESUP 130
   double del,t,*pt,*ptt,*xit;  #define AGEBASE 40
   double fp,fptt;  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
   double *xits;  #ifdef _WIN32
   pt=vector(1,n);  #define DIRSEPARATOR '\\'
   ptt=vector(1,n);  #define CHARSEPARATOR "\\"
   xit=vector(1,n);  #define ODIRSEPARATOR '/'
   xits=vector(1,n);  #else
   *fret=(*func)(p);  #define DIRSEPARATOR '/'
   for (j=1;j<=n;j++) pt[j]=p[j];  #define CHARSEPARATOR "/"
   for (*iter=1;;++(*iter)) {  #define ODIRSEPARATOR '\\'
     fp=(*fret);  #endif
     ibig=0;  
     del=0.0;  /* $Id$ */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /* $State$ */
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
     printf("\n");  char fullversion[]="$Revision$ $Date$"; 
     for (i=1;i<=n;i++) {  char strstart[80];
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       fptt=(*fret);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 #ifdef DEBUG  int nvar=0, nforce=0; /* Number of variables, number of forces */
       printf("fret=%lf \n",*fret);  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
 #endif  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
       printf("%d",i);fflush(stdout);  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
       linmin(p,xit,n,fret,func);  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
       if (fabs(fptt-(*fret)) > del) {  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
         del=fabs(fptt-(*fret));  int cptcovprodnoage=0; /**< Number of covariate products without age */   
         ibig=i;  int cptcoveff=0; /* Total number of covariates to vary for printing results */
       }  int cptcov=0; /* Working variable */
 #ifdef DEBUG  int npar=NPARMAX;
       printf("%d %.12e",i,(*fret));  int nlstate=2; /* Number of live states */
       for (j=1;j<=n;j++) {  int ndeath=1; /* Number of dead states */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
         printf(" x(%d)=%.12e",j,xit[j]);  int popbased=0;
       }  
       for(j=1;j<=n;j++)  int *wav; /* Number of waves for this individuual 0 is possible */
         printf(" p=%.12e",p[j]);  int maxwav=0; /* Maxim number of waves */
       printf("\n");  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
 #endif  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     }  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {                     to the likelihood and the sum of weights (done by funcone)*/
 #ifdef DEBUG  int mle=1, weightopt=0;
       int k[2],l;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       k[0]=1;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       k[1]=-1;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       printf("Max: %.12e",(*func)(p));             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       for (j=1;j<=n;j++)  int countcallfunc=0;  /* Count the number of calls to func */
         printf(" %.12e",p[j]);  double jmean=1; /* Mean space between 2 waves */
       printf("\n");  double **matprod2(); /* test */
       for(l=0;l<=1;l++) {  double **oldm, **newm, **savm; /* Working pointers to matrices */
         for (j=1;j<=n;j++) {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  /*FILE *fic ; */ /* Used in readdata only */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
         }  FILE *ficlog, *ficrespow;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  int globpr=0; /* Global variable for printing or not */
       }  double fretone; /* Only one call to likelihood */
 #endif  long ipmx=0; /* Number of contributions */
   double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
       free_vector(xit,1,n);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       free_vector(xits,1,n);  FILE *ficresilk;
       free_vector(ptt,1,n);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       free_vector(pt,1,n);  FILE *ficresprobmorprev;
       return;  FILE *fichtm, *fichtmcov; /* Html File */
     }  FILE *ficreseij;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  char filerese[FILENAMELENGTH];
     for (j=1;j<=n;j++) {  FILE *ficresstdeij;
       ptt[j]=2.0*p[j]-pt[j];  char fileresstde[FILENAMELENGTH];
       xit[j]=p[j]-pt[j];  FILE *ficrescveij;
       pt[j]=p[j];  char filerescve[FILENAMELENGTH];
     }  FILE  *ficresvij;
     fptt=(*func)(ptt);  char fileresv[FILENAMELENGTH];
     if (fptt < fp) {  FILE  *ficresvpl;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  char fileresvpl[FILENAMELENGTH];
       if (t < 0.0) {  char title[MAXLINE];
         linmin(p,xit,n,fret,func);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
         for (j=1;j<=n;j++) {  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
           xi[j][ibig]=xi[j][n];  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
           xi[j][n]=xit[j];  char command[FILENAMELENGTH];
         }  int  outcmd=0;
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         for(j=1;j<=n;j++)  
           printf(" %.12e",xit[j]);  char filelog[FILENAMELENGTH]; /* Log file */
         printf("\n");  char filerest[FILENAMELENGTH];
 #endif  char fileregp[FILENAMELENGTH];
       }  char popfile[FILENAMELENGTH];
     }  
   }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 }  
   /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
 /**** Prevalence limit ****************/  /* struct timezone tzp; */
   /* extern int gettimeofday(); */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  struct tm tml, *gmtime(), *localtime();
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  extern time_t time();
      matrix by transitions matrix until convergence is reached */  
   struct tm start_time, end_time, curr_time, last_time, forecast_time;
   int i, ii,j,k;  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
   double min, max, maxmin, maxmax,sumnew=0.;  struct tm tm;
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  char strcurr[80], strfor[80];
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  char *endptr;
   long lval;
   for (ii=1;ii<=nlstate+ndeath;ii++)  double dval;
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  #define NR_END 1
     }  #define FREE_ARG char*
   #define FTOL 1.0e-10
    cov[1]=1.;  
    #define NRANSI 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  #define ITMAX 200 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;  #define TOL 2.0e-4 
     /* Covariates have to be included here again */  
      cov[2]=agefin;  #define CGOLD 0.3819660 
    #define ZEPS 1.0e-10 
       for (k=1; k<=cptcovn;k++) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  #define GOLD 1.618034 
       }  #define GLIMIT 100.0 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  #define TINY 1.0e-20 
       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]]];  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  #define rint(a) floor(a+0.5)
   /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
     savm=oldm;  /* #define mytinydouble 1.0e-16 */
     oldm=newm;  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
     maxmax=0.;  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
     for(j=1;j<=nlstate;j++){  /* static double dsqrarg; */
       min=1.;  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
       max=0.;  static double sqrarg;
       for(i=1; i<=nlstate; i++) {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         sumnew=0;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  int agegomp= AGEGOMP;
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  int imx; 
         min=FMIN(min,prlim[i][j]);  int stepm=1;
       }  /* Stepm, step in month: minimum step interpolation*/
       maxmin=max-min;  
       maxmax=FMAX(maxmax,maxmin);  int estepm;
     }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     if(maxmax < ftolpl){  
       return prlim;  int m,nb;
     }  long *num;
   }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
 /*************** transition probabilities ***************/  double *ageexmed,*agecens;
   double dateintmean=0;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  double *weight;
   double s1, s2;  int **s; /* Status */
   /*double t34;*/  double *agedc;
   int i,j,j1, nc, ii, jj;  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
                     * covar=matrix(0,NCOVMAX,1,n); 
     for(i=1; i<= nlstate; i++){                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
     for(j=1; j<i;j++){  double  idx; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
         /*s2 += param[i][j][nc]*cov[nc];*/  int *Ndum; /** Freq of modality (tricode */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  int **codtab; /**< codtab=imatrix(1,100,1,10); */
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
       }  double *lsurv, *lpop, *tpop;
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
     }  double ftolhess; /**< Tolerance for computing hessian */
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /**************** split *************************/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  {
       }    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       ps[i][j]=s2;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     }    */ 
   }    char  *ss;                            /* pointer */
     /*ps[3][2]=1;*/    int   l1, l2;                         /* length counters */
   
   for(i=1; i<= nlstate; i++){    l1 = strlen(path );                   /* length of path */
      s1=0;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     for(j=1; j<i; j++)    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       s1+=exp(ps[i][j]);    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 */
       s1+=exp(ps[i][j]);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     ps[i][i]=1./(s1+1.);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     for(j=1; j<i; j++)      /* get current working directory */
       ps[i][j]= exp(ps[i][j])*ps[i][i];      /*    extern  char* getcwd ( char *buf , int len);*/
     for(j=i+1; j<=nlstate+ndeath; j++)      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
       ps[i][j]= exp(ps[i][j])*ps[i][i];        return( GLOCK_ERROR_GETCWD );
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      }
   } /* end i */      /* got dirc from getcwd*/
       printf(" DIRC = %s \n",dirc);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    } else {                              /* strip direcotry from path */
     for(jj=1; jj<= nlstate+ndeath; jj++){      ss++;                               /* after this, the filename */
       ps[ii][jj]=0;      l2 = strlen( ss );                  /* length of filename */
       ps[ii][ii]=1;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     }      strcpy( name, ss );         /* save file name */
   }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
       printf(" DIRC2 = %s \n",dirc);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    }
     for(jj=1; jj<= nlstate+ndeath; jj++){    /* We add a separator at the end of dirc if not exists */
      printf("%lf ",ps[ii][jj]);    l1 = strlen( dirc );                  /* length of directory */
    }    if( dirc[l1-1] != DIRSEPARATOR ){
     printf("\n ");      dirc[l1] =  DIRSEPARATOR;
     }      dirc[l1+1] = 0; 
     printf("\n ");printf("%lf ",cov[2]);*/      printf(" DIRC3 = %s \n",dirc);
 /*    }
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    ss = strrchr( name, '.' );            /* find last / */
   goto end;*/    if (ss >0){
     return ps;      ss++;
 }      strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
 /**************** Product of 2 matrices ******************/      l2= strlen(ss)+1;
       strncpy( finame, name, l1-l2);
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      finame[l1-l2]= 0;
 {    }
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    return( 0 );                          /* we're done */
   /* 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;  /******************************************/
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)  void replace_back_to_slash(char *s, char*t)
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  {
         out[i][k] +=in[i][j]*b[j][k];    int i;
     int lg=0;
   return out;    i=0;
 }    lg=strlen(t);
     for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
 /************* Higher Matrix Product ***************/      if (t[i]== '\\') s[i]='/';
     }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  }
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  char *trimbb(char *out, char *in)
      duration (i.e. until  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    char *s;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    s=out;
      (typically every 2 years instead of every month which is too big).    while (*in != '\0'){
      Model is determined by parameters x and covariates have to be      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
      included manually here.        in++;
       }
      */      *out++ = *in++;
     }
   int i, j, d, h, k;    *out='\0';
   double **out, cov[NCOVMAX];    return s;
   double **newm;  }
   
   /* Hstepm could be zero and should return the unit matrix */  char *cutl(char *blocc, char *alocc, char *in, char occ)
   for (i=1;i<=nlstate+ndeath;i++)  {
     for (j=1;j<=nlstate+ndeath;j++){    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
       oldm[i][j]=(i==j ? 1.0 : 0.0);       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       po[i][j][0]=(i==j ? 1.0 : 0.0);       gives blocc="abcdef2ghi" and alocc="j".
     }       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    */
   for(h=1; h <=nhstepm; h++){    char *s, *t;
     for(d=1; d <=hstepm; d++){    t=in;s=in;
       newm=savm;    while ((*in != occ) && (*in != '\0')){
       /* Covariates have to be included here again */      *alocc++ = *in++;
       cov[1]=1.;    }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    if( *in == occ){
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      *(alocc)='\0';
       for (k=1; k<=cptcovage;k++)      s=++in;
         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]]];    if (s == t) {/* occ not found */
       *(alocc-(in-s))='\0';
       in=s;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    }
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    while ( *in != '\0'){
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      *blocc++ = *in++;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    }
       savm=oldm;  
       oldm=newm;    *blocc='\0';
     }    return t;
     for(i=1; i<=nlstate+ndeath; i++)  }
       for(j=1;j<=nlstate+ndeath;j++) {  char *cutv(char *blocc, char *alocc, char *in, char occ)
         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]);    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
          */       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       }       gives blocc="abcdef2ghi" and alocc="j".
   } /* end h */       If occ is not found blocc is null and alocc is equal to in. Returns alocc
   return po;    */
 }    char *s, *t;
     t=in;s=in;
     while (*in != '\0'){
 /*************** log-likelihood *************/      while( *in == occ){
 double func( double *x)        *blocc++ = *in++;
 {        s=in;
   int i, ii, j, k, mi, d, kk;      }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      *blocc++ = *in++;
   double **out;    }
   double sw; /* Sum of weights */    if (s == t) /* occ not found */
   double lli; /* Individual log likelihood */      *(blocc-(in-s))='\0';
   long ipmx;    else
   /*extern weight */      *(blocc-(in-s)-1)='\0';
   /* We are differentiating ll according to initial status */    in=s;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    while ( *in != '\0'){
   /*for(i=1;i<imx;i++)      *alocc++ = *in++;
     printf(" %d\n",s[4][i]);    }
   */  
   cov[1]=1.;    *alocc='\0';
     return s;
   for(k=1; k<=nlstate; k++) ll[k]=0.;  }
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  int nbocc(char *s, char occ)
     for(mi=1; mi<= wav[i]-1; mi++){  {
       for (ii=1;ii<=nlstate+ndeath;ii++)    int i,j=0;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    int lg=20;
       for(d=0; d<dh[mi][i]; d++){    i=0;
         newm=savm;    lg=strlen(s);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    for(i=0; i<= lg; i++) {
         for (kk=1; kk<=cptcovage;kk++) {    if  (s[i] == occ ) j++;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    }
         }    return j;
          }
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  /* void cutv(char *u,char *v, char*t, char occ) */
         savm=oldm;  /* { */
         oldm=newm;  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
          /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
          /*      gives u="abcdef2ghi" and v="j" *\/ */
       } /* end mult */  /*   int i,lg,j,p=0; */
        /*   i=0; */
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  /*   lg=strlen(t); */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  /*   for(j=0; j<=lg-1; j++) { */
       ipmx +=1;  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
       sw += weight[i];  /*   } */
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */  /*   for(j=0; j<p; j++) { */
   } /* end of individual */  /*     (u[j] = t[j]); */
   /*   } */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  /*      u[p]='\0'; */
   /* 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 */  /*    for(j=0; j<= lg; j++) { */
   return -l;  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
 }  /*   } */
   /* } */
   
 /*********** Maximum Likelihood Estimation ***************/  #ifdef _WIN32
   char * strsep(char **pp, const char *delim)
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  {
 {    char *p, *q;
   int i,j, iter;           
   double **xi,*delti;    if ((p = *pp) == NULL)
   double fret;      return 0;
   xi=matrix(1,npar,1,npar);    if ((q = strpbrk (p, delim)) != NULL)
   for (i=1;i<=npar;i++)    {
     for (j=1;j<=npar;j++)      *pp = q + 1;
       xi[i][j]=(i==j ? 1.0 : 0.0);      *q = '\0';
   printf("Powell\n");    }
   powell(p,xi,npar,ftol,&iter,&fret,func);    else
       *pp = 0;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    return p;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  }
   #endif
 }  
   /********************** nrerror ********************/
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  void nrerror(char error_text[])
 {  {
   double  **a,**y,*x,pd;    fprintf(stderr,"ERREUR ...\n");
   double **hess;    fprintf(stderr,"%s\n",error_text);
   int i, j,jk;    exit(EXIT_FAILURE);
   int *indx;  }
   /*********************** vector *******************/
   double hessii(double p[], double delta, int theta, double delti[]);  double *vector(int nl, int nh)
   double hessij(double p[], double delti[], int i, int j);  {
   void lubksb(double **a, int npar, int *indx, double b[]) ;    double *v;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
   hess=matrix(1,npar,1,npar);    return v-nl+NR_END;
   }
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){  /************************ free vector ******************/
     printf("%d",i);fflush(stdout);  void free_vector(double*v, int nl, int nh)
     hess[i][i]=hessii(p,ftolhess,i,delti);  {
     /*printf(" %f ",p[i]);*/    free((FREE_ARG)(v+nl-NR_END));
     /*printf(" %lf ",hess[i][i]);*/  }
   }  
    /************************ivector *******************************/
   for (i=1;i<=npar;i++) {  int *ivector(long nl,long nh)
     for (j=1;j<=npar;j++)  {  {
       if (j>i) {    int *v;
         printf(".%d%d",i,j);fflush(stdout);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         hess[i][j]=hessij(p,delti,i,j);    if (!v) nrerror("allocation failure in ivector");
         hess[j][i]=hess[i][j];        return v-nl+NR_END;
         /*printf(" %lf ",hess[i][j]);*/  }
       }  
     }  /******************free ivector **************************/
   }  void free_ivector(int *v, long nl, long nh)
   printf("\n");  {
     free((FREE_ARG)(v+nl-NR_END));
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  }
    
   a=matrix(1,npar,1,npar);  /************************lvector *******************************/
   y=matrix(1,npar,1,npar);  long *lvector(long nl,long nh)
   x=vector(1,npar);  {
   indx=ivector(1,npar);    long *v;
   for (i=1;i<=npar;i++)    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    if (!v) nrerror("allocation failure in ivector");
   ludcmp(a,npar,indx,&pd);    return v-nl+NR_END;
   }
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  /******************free lvector **************************/
     x[j]=1;  void free_lvector(long *v, long nl, long nh)
     lubksb(a,npar,indx,x);  {
     for (i=1;i<=npar;i++){    free((FREE_ARG)(v+nl-NR_END));
       matcov[i][j]=x[i];  }
     }  
   }  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
   printf("\n#Hessian matrix#\n");       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   for (i=1;i<=npar;i++) {  { 
     for (j=1;j<=npar;j++) {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       printf("%.3e ",hess[i][j]);    int **m; 
     }    
     printf("\n");    /* allocate pointers to rows */ 
   }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
   /* Recompute Inverse */    m += NR_END; 
   for (i=1;i<=npar;i++)    m -= nrl; 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    
   ludcmp(a,npar,indx,&pd);    
     /* allocate rows and set pointers to them */ 
   /*  printf("\n#Hessian matrix recomputed#\n");    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   for (j=1;j<=npar;j++) {    m[nrl] += NR_END; 
     for (i=1;i<=npar;i++) x[i]=0;    m[nrl] -= ncl; 
     x[j]=1;    
     lubksb(a,npar,indx,x);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     for (i=1;i<=npar;i++){    
       y[i][j]=x[i];    /* return pointer to array of pointers to rows */ 
       printf("%.3e ",y[i][j]);    return m; 
     }  } 
     printf("\n");  
   }  /****************** free_imatrix *************************/
   */  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
   free_matrix(a,1,npar,1,npar);        long nch,ncl,nrh,nrl; 
   free_matrix(y,1,npar,1,npar);       /* free an int matrix allocated by imatrix() */ 
   free_vector(x,1,npar);  { 
   free_ivector(indx,1,npar);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   free_matrix(hess,1,npar,1,npar);    free((FREE_ARG) (m+nrl-NR_END)); 
   } 
   
 }  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
 /*************** hessian matrix ****************/  {
 double hessii( double x[], double delta, int theta, double delti[])    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 {    double **m;
   int i;  
   int l=1, lmax=20;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double k1,k2;    if (!m) nrerror("allocation failure 1 in matrix()");
   double p2[NPARMAX+1];    m += NR_END;
   double res;    m -= nrl;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  
   double fx;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   int k=0,kmax=10;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double l1;    m[nrl] += NR_END;
     m[nrl] -= ncl;
   fx=func(x);  
   for (i=1;i<=npar;i++) p2[i]=x[i];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for(l=0 ; l <=lmax; l++){    return m;
     l1=pow(10,l);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     delts=delt;  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
     for(k=1 ; k <kmax; k=k+1){  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
       delt = delta*(l1*k);     */
       p2[theta]=x[theta] +delt;  }
       k1=func(p2)-fx;  
       p2[theta]=x[theta]-delt;  /*************************free matrix ************************/
       k2=func(p2)-fx;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       /*res= (k1-2.0*fx+k2)/delt/delt; */  {
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    free((FREE_ARG)(m[nrl]+ncl-NR_END));
          free((FREE_ARG)(m+nrl-NR_END));
 #ifdef DEBUG  }
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  
 #endif  /******************* ma3x *******************************/
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  {
         k=kmax;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       }    double ***m;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  
         k=kmax; l=lmax*10.;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       }    if (!m) nrerror("allocation failure 1 in matrix()");
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    m += NR_END;
         delts=delt;    m -= nrl;
       }  
     }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   delti[theta]=delts;    m[nrl] += NR_END;
   return res;    m[nrl] -= ncl;
    
 }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   
 double hessij( double x[], double delti[], int thetai,int thetaj)    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   int i;    m[nrl][ncl] += NR_END;
   int l=1, l1, lmax=20;    m[nrl][ncl] -= nll;
   double k1,k2,k3,k4,res,fx;    for (j=ncl+1; j<=nch; j++) 
   double p2[NPARMAX+1];      m[nrl][j]=m[nrl][j-1]+nlay;
   int k;    
     for (i=nrl+1; i<=nrh; i++) {
   fx=func(x);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   for (k=1; k<=2; k++) {      for (j=ncl+1; j<=nch; j++) 
     for (i=1;i<=npar;i++) p2[i]=x[i];        m[i][j]=m[i][j-1]+nlay;
     p2[thetai]=x[thetai]+delti[thetai]/k;    }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    return m; 
     k1=func(p2)-fx;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
               &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     p2[thetai]=x[thetai]+delti[thetai]/k;    */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  }
     k2=func(p2)-fx;  
    /*************************free ma3x ************************/
     p2[thetai]=x[thetai]-delti[thetai]/k;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  {
     k3=func(p2)-fx;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
      free((FREE_ARG)(m[nrl]+ncl-NR_END));
     p2[thetai]=x[thetai]-delti[thetai]/k;    free((FREE_ARG)(m+nrl-NR_END));
     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 */  /*************** function subdirf ***********/
 #ifdef DEBUG  char *subdirf(char fileres[])
     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);  {
 #endif    /* Caution optionfilefiname is hidden */
   }    strcpy(tmpout,optionfilefiname);
   return res;    strcat(tmpout,"/"); /* Add to the right */
 }    strcat(tmpout,fileres);
     return tmpout;
 /************** Inverse of matrix **************/  }
 void ludcmp(double **a, int n, int *indx, double *d)  
 {  /*************** function subdirf2 ***********/
   int i,imax,j,k;  char *subdirf2(char fileres[], char *preop)
   double big,dum,sum,temp;  {
   double *vv;    
      /* Caution optionfilefiname is hidden */
   vv=vector(1,n);    strcpy(tmpout,optionfilefiname);
   *d=1.0;    strcat(tmpout,"/");
   for (i=1;i<=n;i++) {    strcat(tmpout,preop);
     big=0.0;    strcat(tmpout,fileres);
     for (j=1;j<=n;j++)    return tmpout;
       if ((temp=fabs(a[i][j])) > big) big=temp;  }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  
     vv[i]=1.0/big;  /*************** function subdirf3 ***********/
   }  char *subdirf3(char fileres[], char *preop, char *preop2)
   for (j=1;j<=n;j++) {  {
     for (i=1;i<j;i++) {    
       sum=a[i][j];    /* Caution optionfilefiname is hidden */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    strcpy(tmpout,optionfilefiname);
       a[i][j]=sum;    strcat(tmpout,"/");
     }    strcat(tmpout,preop);
     big=0.0;    strcat(tmpout,preop2);
     for (i=j;i<=n;i++) {    strcat(tmpout,fileres);
       sum=a[i][j];    return tmpout;
       for (k=1;k<j;k++)  }
         sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  char *asc_diff_time(long time_sec, char ascdiff[])
       if ( (dum=vv[i]*fabs(sum)) >= big) {  {
         big=dum;    long sec_left, days, hours, minutes;
         imax=i;    days = (time_sec) / (60*60*24);
       }    sec_left = (time_sec) % (60*60*24);
     }    hours = (sec_left) / (60*60) ;
     if (j != imax) {    sec_left = (sec_left) %(60*60);
       for (k=1;k<=n;k++) {    minutes = (sec_left) /60;
         dum=a[imax][k];    sec_left = (sec_left) % (60);
         a[imax][k]=a[j][k];    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
         a[j][k]=dum;    return ascdiff;
       }  }
       *d = -(*d);  
       vv[imax]=vv[j];  /***************** f1dim *************************/
     }  extern int ncom; 
     indx[j]=imax;  extern double *pcom,*xicom;
     if (a[j][j] == 0.0) a[j][j]=TINY;  extern double (*nrfunc)(double []); 
     if (j != n) {   
       dum=1.0/(a[j][j]);  double f1dim(double x) 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  { 
     }    int j; 
   }    double f;
   free_vector(vv,1,n);  /* Doesn't work */    double *xt; 
 ;   
 }    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 void lubksb(double **a, int n, int *indx, double b[])    f=(*nrfunc)(xt); 
 {    free_vector(xt,1,ncom); 
   int i,ii=0,ip,j;    return f; 
   double sum;  } 
    
   for (i=1;i<=n;i++) {  /*****************brent *************************/
     ip=indx[i];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     sum=b[ip];  { 
     b[ip]=b[i];    int iter; 
     if (ii)    double a,b,d,etemp;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    double fu=0,fv,fw,fx;
     else if (sum) ii=i;    double ftemp=0.;
     b[i]=sum;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   }    double e=0.0; 
   for (i=n;i>=1;i--) {   
     sum=b[i];    a=(ax < cx ? ax : cx); 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    b=(ax > cx ? ax : cx); 
     b[i]=sum/a[i][i];    x=w=v=bx; 
   }    fw=fv=fx=(*f)(x); 
 }    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
 /************ Frequencies ********************/      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 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)      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 {  /* Some frequencies */      printf(".");fflush(stdout);
        fprintf(ficlog,".");fflush(ficlog);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  #ifdef DEBUGBRENT
   double ***freq; /* Frequencies */      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   double *pp;      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);
   double pos, k2, dateintsum=0,k2cpt=0;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   FILE *ficresp;  #endif
   char fileresp[FILENAMELENGTH];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
          *xmin=x; 
   pp=vector(1,nlstate);        return fx; 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      } 
   strcpy(fileresp,"p");      ftemp=fu;
   strcat(fileresp,fileres);      if (fabs(e) > tol1) { 
   if((ficresp=fopen(fileresp,"w"))==NULL) {        r=(x-w)*(fx-fv); 
     printf("Problem with prevalence resultfile: %s\n", fileresp);        q=(x-v)*(fx-fw); 
     exit(0);        p=(x-v)*q-(x-w)*r; 
   }        q=2.0*(q-r); 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        if (q > 0.0) p = -p; 
   j1=0;        q=fabs(q); 
          etemp=e; 
   j=cptcoveff;        e=d; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        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)); 
   for(k1=1; k1<=j;k1++){        else { 
     for(i1=1; i1<=ncodemax[k1];i1++){          d=p/q; 
       j1++;          u=x+d; 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          if (u-a < tol2 || b-u < tol2) 
         scanf("%d", i);*/            d=SIGN(tol1,xm-x); 
       for (i=-1; i<=nlstate+ndeath; i++)          } 
         for (jk=-1; jk<=nlstate+ndeath; jk++)        } else { 
           for(m=agemin; m <= agemax+3; m++)        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
             freq[i][jk][m]=0;      } 
            u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       dateintsum=0;      fu=(*f)(u); 
       k2cpt=0;      if (fu <= fx) { 
       for (i=1; i<=imx; i++) {        if (u >= x) a=x; else b=x; 
         bool=1;        SHFT(v,w,x,u) 
         if  (cptcovn>0) {          SHFT(fv,fw,fx,fu) 
           for (z1=1; z1<=cptcoveff; z1++)          } else { 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            if (u < x) a=u; else b=u; 
               bool=0;            if (fu <= fw || w == x) { 
         }              v=w; 
         if (bool==1) {              w=u; 
           for(m=firstpass; m<=lastpass; m++){              fv=fw; 
             k2=anint[m][i]+(mint[m][i]/12.);              fw=fu; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            } else if (fu <= fv || v == x || v == w) { 
               if(agev[m][i]==0) agev[m][i]=agemax+1;              v=u; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;              fv=fu; 
               if (m<lastpass) {            } 
                 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];    } 
               }    nrerror("Too many iterations in brent"); 
                  *xmin=x; 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    return fx; 
                 dateintsum=dateintsum+k2;  } 
                 k2cpt++;  
               }  /****************** mnbrak ***********************/
             }  
           }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         }              double (*func)(double)) 
       }  { 
            double ulim,u,r,q, dum;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    double fu; 
    
       if  (cptcovn>0) {    *fa=(*func)(*ax); 
         fprintf(ficresp, "\n#********** Variable ");    *fb=(*func)(*bx); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    if (*fb > *fa) { 
         fprintf(ficresp, "**********\n#");      SHFT(dum,*ax,*bx,dum) 
       }        SHFT(dum,*fb,*fa,dum) 
       for(i=1; i<=nlstate;i++)        } 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    *cx=(*bx)+GOLD*(*bx-*ax); 
       fprintf(ficresp, "\n");    *fc=(*func)(*cx); 
          while (*fb > *fc) { /* Declining fa, fb, fc */
       for(i=(int)agemin; i <= (int)agemax+3; i++){      r=(*bx-*ax)*(*fb-*fc); 
         if(i==(int)agemax+3)      q=(*bx-*cx)*(*fb-*fa); 
           printf("Total");      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         else        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
           printf("Age %d", i);      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
         for(jk=1; jk <=nlstate ; jk++){      if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        fu=(*func)(u); 
             pp[jk] += freq[jk][m][i];  #ifdef DEBUG
         }        /* f(x)=A(x-u)**2+f(u) */
         for(jk=1; jk <=nlstate ; jk++){        double A, fparabu; 
           for(m=-1, pos=0; m <=0 ; m++)        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
             pos += freq[jk][m][i];        fparabu= *fa - A*(*ax-u)*(*ax-u);
           if(pp[jk]>=1.e-10)        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);
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        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);
           else  #endif 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
         }        fu=(*func)(u); 
         if (fu < *fc) { 
         for(jk=1; jk <=nlstate ; jk++){          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            SHFT(*fb,*fc,fu,(*func)(u)) 
             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,pos=0; jk <=nlstate ; jk++)        fu=(*func)(u); 
           pos += pp[jk];      } else { 
         for(jk=1; jk <=nlstate ; jk++){        u=(*cx)+GOLD*(*cx-*bx); 
           if(pos>=1.e-5)        fu=(*func)(u); 
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      } 
           else      SHFT(*ax,*bx,*cx,u) 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        SHFT(*fa,*fb,*fc,fu) 
           if( i <= (int) agemax){        } 
             if(pos>=1.e-5){  } 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  
               probs[i][jk][j1]= pp[jk]/pos;  /*************** linmin ************************/
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  /* 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 ,
             else  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  the value of func at the returned location p . This is actually all accomplished by calling the
           }  routines mnbrak and brent .*/
         }  int ncom; 
          double *pcom,*xicom;
         for(jk=-1; jk <=nlstate+ndeath; jk++)  double (*nrfunc)(double []); 
           for(m=-1; m <=nlstate+ndeath; m++)   
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         if(i <= (int) agemax)  { 
           fprintf(ficresp,"\n");    double brent(double ax, double bx, double cx, 
         printf("\n");                 double (*f)(double), double tol, double *xmin); 
       }    double f1dim(double x); 
     }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   }                double *fc, double (*func)(double)); 
   dateintmean=dateintsum/k2cpt;    int j; 
      double xx,xmin,bx,ax; 
   fclose(ficresp);    double fx,fb,fa;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);   
   free_vector(pp,1,nlstate);    ncom=n; 
      pcom=vector(1,n); 
   /* End of Freq */    xicom=vector(1,n); 
 }    nrfunc=func; 
     for (j=1;j<=n;j++) { 
 /************ Prevalence ********************/      pcom[j]=p[j]; 
 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)      xicom[j]=xi[j]; 
 {  /* Some frequencies */    } 
      ax=0.0; 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    xx=1.0; 
   double ***freq; /* Frequencies */    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
   double *pp;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
   double pos, k2;  #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   pp=vector(1,nlstate);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  #endif
      for (j=1;j<=n;j++) { 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      xi[j] *= xmin; 
   j1=0;      p[j] += xi[j]; 
      } 
   j=cptcoveff;    free_vector(xicom,1,n); 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    free_vector(pcom,1,n); 
    } 
   for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){  
       j1++;  /*************** powell ************************/
        /*
       for (i=-1; i<=nlstate+ndeath; i++)    Minimization of a function func of n variables. Input consists of an initial starting point
         for (jk=-1; jk<=nlstate+ndeath; jk++)    p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
           for(m=agemin; m <= agemax+3; m++)  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
             freq[i][jk][m]=0;  such that failure to decrease by more than this amount on one iteration signals doneness. On
        output, p is set to the best point found, xi is the then-current direction set, fret is the returned
       for (i=1; i<=imx; i++) {  function value at p , and iter is the number of iterations taken. The routine linmin is used.
         bool=1;   */
         if  (cptcovn>0) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
           for (z1=1; z1<=cptcoveff; z1++)              double (*func)(double [])) 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  { 
               bool=0;    void linmin(double p[], double xi[], int n, double *fret, 
         }                double (*func)(double [])); 
         if (bool==1) {    int i,ibig,j; 
           for(m=firstpass; m<=lastpass; m++){    double del,t,*pt,*ptt,*xit;
             k2=anint[m][i]+(mint[m][i]/12.);    double fp,fptt;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    double *xits;
               if(agev[m][i]==0) agev[m][i]=agemax+1;    int niterf, itmp;
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {    pt=vector(1,n); 
                 if (calagedate>0)    ptt=vector(1,n); 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    xit=vector(1,n); 
                 else    xits=vector(1,n); 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    *fret=(*func)(p); 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    for (j=1;j<=n;j++) pt[j]=p[j]; 
               }      rcurr_time = time(NULL);  
             }    for (*iter=1;;++(*iter)) { 
           }      fp=(*fret); 
         }      ibig=0; 
       }      del=0.0; 
       for(i=(int)agemin; i <= (int)agemax+3; i++){      rlast_time=rcurr_time;
         for(jk=1; jk <=nlstate ; jk++){      /* (void) gettimeofday(&curr_time,&tzp); */
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      rcurr_time = time(NULL);  
             pp[jk] += freq[jk][m][i];      curr_time = *localtime(&rcurr_time);
         }      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
         for(jk=1; jk <=nlstate ; jk++){      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
           for(m=-1, pos=0; m <=0 ; m++)  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
             pos += freq[jk][m][i];     for (i=1;i<=n;i++) {
         }        printf(" %d %.12f",i, p[i]);
                fprintf(ficlog," %d %.12lf",i, p[i]);
         for(jk=1; jk <=nlstate ; jk++){        fprintf(ficrespow," %.12lf", p[i]);
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      }
             pp[jk] += freq[jk][m][i];      printf("\n");
         }      fprintf(ficlog,"\n");
              fprintf(ficrespow,"\n");fflush(ficrespow);
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      if(*iter <=3){
                tml = *localtime(&rcurr_time);
         for(jk=1; jk <=nlstate ; jk++){            strcpy(strcurr,asctime(&tml));
           if( i <= (int) agemax){        rforecast_time=rcurr_time; 
             if(pos>=1.e-5){        itmp = strlen(strcurr);
               probs[i][jk][j1]= pp[jk]/pos;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
             }          strcurr[itmp-1]='\0';
           }        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
         }        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
                for(niterf=10;niterf<=30;niterf+=10){
       }          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
     }          forecast_time = *localtime(&rforecast_time);
   }          strcpy(strfor,asctime(&forecast_time));
           itmp = strlen(strfor);
            if(strfor[itmp-1]=='\n')
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          strfor[itmp-1]='\0';
   free_vector(pp,1,nlstate);          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);
            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);
 }  /* End of Freq */        }
       }
 /************* Waves Concatenation ***************/      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][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)        fptt=(*fret); 
 {  #ifdef DEBUG
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
      Death is a valid wave (if date is known).            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  #endif
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        printf("%d",i);fflush(stdout);
      and mw[mi+1][i]. dh depends on stepm.        fprintf(ficlog,"%d",i);fflush(ficlog);
      */        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
   int i, mi, m;          del=fabs(fptt-(*fret)); 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          ibig=i; 
      double sum=0., jmean=0.;*/        } 
   #ifdef DEBUG
   int j, k=0,jk, ju, jl;        printf("%d %.12e",i,(*fret));
   double sum=0.;        fprintf(ficlog,"%d %.12e",i,(*fret));
   jmin=1e+5;        for (j=1;j<=n;j++) {
   jmax=-1;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   jmean=0.;          printf(" x(%d)=%.12e",j,xit[j]);
   for(i=1; i<=imx; i++){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     mi=0;        }
     m=firstpass;        for(j=1;j<=n;j++) {
     while(s[m][i] <= nlstate){          printf(" p(%d)=%.12e",j,p[j]);
       if(s[m][i]>=1)          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
         mw[++mi][i]=m;        }
       if(m >=lastpass)        printf("\n");
         break;        fprintf(ficlog,"\n");
       else  #endif
         m++;      } /* end i */
     }/* end while */      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     if (s[m][i] > nlstate){  #ifdef DEBUG
       mi++;     /* Death is another wave */        int k[2],l;
       /* if(mi==0)  never been interviewed correctly before death */        k[0]=1;
          /* Only death is a correct wave */        k[1]=-1;
       mw[mi][i]=m;        printf("Max: %.12e",(*func)(p));
     }        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
     wav[i]=mi;          printf(" %.12e",p[j]);
     if(mi==0)          fprintf(ficlog," %.12e",p[j]);
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        }
   }        printf("\n");
         fprintf(ficlog,"\n");
   for(i=1; i<=imx; i++){        for(l=0;l<=1;l++) {
     for(mi=1; mi<wav[i];mi++){          for (j=1;j<=n;j++) {
       if (stepm <=0)            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         dh[mi][i]=1;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       else{            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         if (s[mw[mi+1][i]][i] > nlstate) {          }
           if (agedc[i] < 2*AGESUP) {          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           if(j==0) j=1;  /* Survives at least one month after exam */        }
           k=k+1;  #endif
           if (j >= jmax) jmax=j;  
           if (j <= jmin) jmin=j;  
           sum=sum+j;        free_vector(xit,1,n); 
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        free_vector(xits,1,n); 
           }        free_vector(ptt,1,n); 
         }        free_vector(pt,1,n); 
         else{        return; 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      } 
           k=k+1;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
           if (j >= jmax) jmax=j;      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
           else if (j <= jmin)jmin=j;        ptt[j]=2.0*p[j]-pt[j]; 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        xit[j]=p[j]-pt[j]; 
           sum=sum+j;        pt[j]=p[j]; 
         }      } 
         jk= j/stepm;      fptt=(*func)(ptt); 
         jl= j -jk*stepm;      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
         ju= j -(jk+1)*stepm;        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
         if(jl <= -ju)        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
           dh[mi][i]=jk;        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
         else        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
           dh[mi][i]=jk+1;        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
         if(dh[mi][i]==0)        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
           dh[mi][i]=1; /* At least one step */        /* Thus we compare delta(2h) with observed f1-f3 */
       }        /* or best gain on one ancient line 'del' with total  */
     }        /* gain f1-f2 = f1 - f2 - 'del' with del  */
   }        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   jmean=sum/k;  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
  }        t= t- del*SQR(fp-fptt);
 /*********** Tricode ****************************/        printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
 void tricode(int *Tvar, int **nbcode, int imx)        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);
 {  #ifdef DEBUG
   int Ndum[20],ij=1, k, j, i;        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
   int cptcode=0;               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   cptcoveff=0;        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                 (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   for (k=0; k<19; k++) Ndum[k]=0;        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);
   for (k=1; k<=7; k++) ncodemax[k]=0;        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
   #endif
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {        if (t < 0.0) { /* Then we use it for last direction */
     for (i=1; i<=imx; i++) {          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
       ij=(int)(covar[Tvar[j]][i]);          for (j=1;j<=n;j++) { 
       Ndum[ij]++;            xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
       if (ij > cptcode) cptcode=ij;          }
     }          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
           fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;  #ifdef DEBUG
     }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     ij=1;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
     for (i=1; i<=ncodemax[j]; i++) {            fprintf(ficlog," %.12e",xit[j]);
       for (k=0; k<=19; k++) {          }
         if (Ndum[k] != 0) {          printf("\n");
           nbcode[Tvar[j]][ij]=k;          fprintf(ficlog,"\n");
            #endif
           ij++;        } /* end of t negative */
         }      } /* end if (fptt < fp)  */
         if (ij > ncodemax[j]) break;    } 
       }    } 
     }  
   }    /**** Prevalence limit (stable or period prevalence)  ****************/
   
  for (k=0; k<19; k++) Ndum[k]=0;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   {
  for (i=1; i<=ncovmodel-2; i++) {    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       ij=Tvar[i];       matrix by transitions matrix until convergence is reached */
       Ndum[ij]++;    
     }    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
  ij=1;    /* double **matprod2(); */ /* test */
  for (i=1; i<=10; i++) {    double **out, cov[NCOVMAX+1], **pmij();
    if((Ndum[i]!=0) && (i<=ncovcol)){    double **newm;
      Tvaraff[ij]=i;    double agefin, delaymax=50 ; /* Max number of years to converge */
      ij++;    
    }    for (ii=1;ii<=nlstate+ndeath;ii++)
  }      for (j=1;j<=nlstate+ndeath;j++){
          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     cptcoveff=ij-1;      }
 }    
     cov[1]=1.;
 /*********** Health Expectancies ****************/    
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
 {      /* Covariates have to be included here again */
   /* Health expectancies */      cov[2]=agefin;
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;      
   double age, agelim, hf;      for (k=1; k<=cptcovn;k++) {
   double ***p3mat,***varhe;        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double **dnewm,**doldm;        /*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]]);*/
   double *xp;      }
   double **gp, **gm;      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   double ***gradg, ***trgradg;      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
   int theta;      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
       
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   xp=vector(1,npar);      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   dnewm=matrix(1,nlstate*2,1,npar);      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   doldm=matrix(1,nlstate*2,1,nlstate*2);      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
        /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
   fprintf(ficreseij,"# Health expectancies\n");      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
   fprintf(ficreseij,"# Age");      
   for(i=1; i<=nlstate;i++)      savm=oldm;
     for(j=1; j<=nlstate;j++)      oldm=newm;
       fprintf(ficreseij," %1d-%1d (SE)",i,j);      maxmax=0.;
   fprintf(ficreseij,"\n");      for(j=1;j<=nlstate;j++){
         min=1.;
   if(estepm < stepm){        max=0.;
     printf ("Problem %d lower than %d\n",estepm, stepm);        for(i=1; i<=nlstate; i++) {
   }          sumnew=0;
   else  hstepm=estepm;            for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   /* We compute the life expectancy from trapezoids spaced every estepm months          prlim[i][j]= newm[i][j]/(1-sumnew);
    * This is mainly to measure the difference between two models: for example          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
    * if stepm=24 months pijx are given only every 2 years and by summing them          max=FMAX(max,prlim[i][j]);
    * we are calculating an estimate of the Life Expectancy assuming a linear          min=FMIN(min,prlim[i][j]);
    * progression inbetween and thus overestimating or underestimating according        }
    * to the curvature of the survival function. If, for the same date, we        maxmin=max-min;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        maxmax=FMAX(maxmax,maxmin);
    * to compare the new estimate of Life expectancy with the same linear      } /* j loop */
    * hypothesis. A more precise result, taking into account a more precise      if(maxmax < ftolpl){
    * curvature will be obtained if estepm is as small as stepm. */        return prlim;
       }
   /* For example we decided to compute the life expectancy with the smallest unit */    } /* age loop */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    return prlim; /* should not reach here */
      nhstepm is the number of hstepm from age to agelim  }
      nstepm is the number of stepm from age to agelin.  
      Look at hpijx to understand the reason of that which relies in memory size  /*************** transition probabilities ***************/ 
      and note for a fixed period like estepm months */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
      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    /* According to parameters values stored in x and the covariate's values stored in cov,
      you sum them up and add 1 year (area under the trapezoids) you won't get the same       computes the probability to be observed in state j being in state i by appying the
      results. So we changed our mind and took the option of the best precision.       model to the ncovmodel covariates (including constant and age).
   */       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
        ncth covariate in the global vector x is given by the formula:
   agelim=AGESUP;       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
     /* nhstepm age range expressed in number of stepm */       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
     nstepm=(int) rint((agelim-age)*YEARM/stepm);       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */       Outputs ps[i][j] the probability to be observed in j being in j according to
     /* if (stepm >= YEARM) hstepm=1;*/       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double s1, lnpijopii;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    /*double t34;*/
     gp=matrix(0,nhstepm,1,nlstate*2);    int i,j, nc, ii, jj;
     gm=matrix(0,nhstepm,1,nlstate*2);  
       for(i=1; i<= nlstate; i++){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        for(j=1; j<i;j++){
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              /*lnpijopii += param[i][j][nc]*cov[nc];*/
              lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
   /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     /* Computing Variances of health expectancies */  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         }
      for(theta=1; theta <=npar; theta++){        for(j=i+1; j<=nlstate+ndeath;j++){
       for(i=1; i<=npar; i++){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            /*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];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
            }
       cptj=0;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       for(j=1; j<= nlstate; j++){        }
         for(i=1; i<=nlstate; i++){      }
           cptj=cptj+1;      
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      for(i=1; i<= nlstate; i++){
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        s1=0;
           }        for(j=1; j<i; j++){
         }          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       }          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
              }
              for(j=i+1; j<=nlstate+ndeath; j++){
       for(i=1; i<=npar; i++)          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          }
              /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
       cptj=0;        ps[i][i]=1./(s1+1.);
       for(j=1; j<= nlstate; j++){        /* Computing other pijs */
         for(i=1;i<=nlstate;i++){        for(j=1; j<i; j++)
           cptj=cptj+1;          ps[i][j]= exp(ps[i][j])*ps[i][i];
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){        for(j=i+1; j<=nlstate+ndeath; j++)
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          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(j=1; j<= nlstate*2; j++)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         for(h=0; h<=nhstepm-1; h++){        for(jj=1; jj<= nlstate+ndeath; jj++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          ps[ii][jj]=0;
         }          ps[ii][ii]=1;
      }        }
          }
 /* End theta */      
       
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
       /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
      for(h=0; h<=nhstepm-1; h++)      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       for(j=1; j<=nlstate*2;j++)      /*   } */
         for(theta=1; theta <=npar; theta++)      /*   printf("\n "); */
           trgradg[h][j][theta]=gradg[h][theta][j];      /* } */
            /* printf("\n ");printf("%lf ",cov[2]);*/
       /*
      for(i=1;i<=nlstate*2;i++)        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       for(j=1;j<=nlstate*2;j++)        goto end;*/
         varhe[i][j][(int)age] =0.;      return ps;
   }
      printf("%d|",(int)age);fflush(stdout);  
      for(h=0;h<=nhstepm-1;h++){  /**************** Product of 2 matrices ******************/
       for(k=0;k<=nhstepm-1;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);  {
         for(i=1;i<=nlstate*2;i++)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
           for(j=1;j<=nlstate*2;j++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    /* 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 */
     /* Computing expectancies */    int i, j, k;
     for(i=1; i<=nlstate;i++)    for(i=nrl; i<= nrh; i++)
       for(j=1; j<=nlstate;j++)      for(k=ncolol; k<=ncoloh; k++){
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        out[i][k]=0.;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        for(j=ncl; j<=nch; j++)
                    out[i][k] +=in[i][j]*b[j][k];
 /* 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]);*/      }
     return out;
         }  }
   
     fprintf(ficreseij,"%3.0f",age );  
     cptj=0;  /************* Higher Matrix Product ***************/
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         cptj++;  {
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );    /* Computes the transition matrix starting at age 'age' over 
       }       'nhstepm*hstepm*stepm' months (i.e. until
     fprintf(ficreseij,"\n");       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           nhstepm*hstepm matrices. 
     free_matrix(gm,0,nhstepm,1,nlstate*2);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     free_matrix(gp,0,nhstepm,1,nlstate*2);       (typically every 2 years instead of every month which is too big 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);       for the memory).
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);       Model is determined by parameters x and covariates have to be 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       included manually here. 
   }  
   printf("\n");       */
   
   free_vector(xp,1,npar);    int i, j, d, h, k;
   free_matrix(dnewm,1,nlstate*2,1,npar);    double **out, cov[NCOVMAX+1];
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    double **newm;
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);  
 }    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
 /************ Variance ******************/      for (j=1;j<=nlstate+ndeath;j++){
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)        oldm[i][j]=(i==j ? 1.0 : 0.0);
 {        po[i][j][0]=(i==j ? 1.0 : 0.0);
   /* Variance of health expectancies */      }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   double **newm;    for(h=1; h <=nhstepm; h++){
   double **dnewm,**doldm;      for(d=1; d <=hstepm; d++){
   int i, j, nhstepm, hstepm, h, nstepm ;        newm=savm;
   int k, cptcode;        /* Covariates have to be included here again */
   double *xp;        cov[1]=1.;
   double **gp, **gm;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double ***gradg, ***trgradg;        for (k=1; k<=cptcovn;k++) 
   double ***p3mat;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double age,agelim, hf;        for (k=1; k<=cptcovage;k++)
   int theta;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   fprintf(ficresvij,"# Age");  
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   fprintf(ficresvij,"\n");        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
   xp=vector(1,npar);        savm=oldm;
   dnewm=matrix(1,nlstate,1,npar);        oldm=newm;
   doldm=matrix(1,nlstate,1,nlstate);      }
        for(i=1; i<=nlstate+ndeath; i++)
   if(estepm < stepm){        for(j=1;j<=nlstate+ndeath;j++) {
     printf ("Problem %d lower than %d\n",estepm, stepm);          po[i][j][h]=newm[i][j];
   }          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   else  hstepm=estepm;          }
   /* For example we decided to compute the life expectancy with the smallest unit */      /*printf("h=%d ",h);*/
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    } /* end h */
      nhstepm is the number of hstepm from age to agelim  /*     printf("\n H=%d \n",h); */
      nstepm is the number of stepm from age to agelin.    return po;
      Look at hpijx to understand the reason of that which relies in memory size  }
      and note for a fixed period like k years */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  #ifdef NLOPT
      survival function given by stepm (the optimization length). Unfortunately it    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
      means that if the survival funtion is printed only each two years of age and if    double fret;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    double *xt;
      results. So we changed our mind and took the option of the best precision.    int j;
   */    myfunc_data *d2 = (myfunc_data *) pd;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  /* xt = (p1-1); */
   agelim = AGESUP;    xt=vector(1,n); 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    printf("Function = %.12lf ",fret);
     gp=matrix(0,nhstepm,1,nlstate);    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     gm=matrix(0,nhstepm,1,nlstate);    printf("\n");
    free_vector(xt,1,n);
     for(theta=1; theta <=npar; theta++){    return fret;
       for(i=1; i<=npar; i++){ /* Computes gradient */  }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  #endif
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    /*************** log-likelihood *************/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  double func( double *x)
   {
       if (popbased==1) {    int i, ii, j, k, mi, d, kk;
         for(i=1; i<=nlstate;i++)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
           prlim[i][i]=probs[(int)age][i][ij];    double **out;
       }    double sw; /* Sum of weights */
      double lli; /* Individual log likelihood */
       for(j=1; j<= nlstate; j++){    int s1, s2;
         for(h=0; h<=nhstepm; h++){    double bbh, survp;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    long ipmx;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    /*extern weight */
         }    /* We are differentiating ll according to initial status */
       }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
        /*for(i=1;i<imx;i++) 
       for(i=1; i<=npar; i++) /* Computes gradient */      printf(" %d\n",s[4][i]);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    ++countcallfunc;
    
       if (popbased==1) {    cov[1]=1.;
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];    for(k=1; k<=nlstate; k++) ll[k]=0.;
       }  
     if(mle==1){
       for(j=1; j<= nlstate; j++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(h=0; h<=nhstepm; h++){        /* Computes the values of the ncovmodel covariates of the model
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];           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 (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
       for(j=1; j<= nlstate; j++)          cov[2+k]=covar[Tvar[k]][i];
         for(h=0; h<=nhstepm; h++){        }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        /* 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] 
     } /* End theta */           has been calculated etc */
         for(mi=1; mi<= wav[i]-1; mi++){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
     for(h=0; h<=nhstepm; h++)              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(theta=1; theta <=npar; theta++)            }
           trgradg[h][j][theta]=gradg[h][theta][j];          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(i=1;i<=nlstate;i++)            for (kk=1; kk<=cptcovage;kk++) {
       for(j=1;j<=nlstate;j++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
         vareij[i][j][(int)age] =0.;            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(h=0;h<=nhstepm;h++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(k=0;k<=nhstepm;k++){            savm=oldm;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);            oldm=newm;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          } /* end mult */
         for(i=1;i<=nlstate;i++)        
           for(j=1;j<=nlstate;j++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          /* But now since version 0.9 we anticipate for bias at large stepm.
       }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     }           * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
     fprintf(ficresvij,"%.0f ",age );           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     for(i=1; i<=nlstate;i++)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       for(j=1; j<=nlstate;j++){           * probability in order to take into account the bias as a fraction of the way
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       }           * -stepm/2 to stepm/2 .
     fprintf(ficresvij,"\n");           * For stepm=1 the results are the same as for previous versions of Imach.
     free_matrix(gp,0,nhstepm,1,nlstate);           * For stepm > 1 the results are less biased than in previous versions. 
     free_matrix(gm,0,nhstepm,1,nlstate);           */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          s1=s[mw[mi][i]][i];
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          s2=s[mw[mi+1][i]][i];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          bbh=(double)bh[mi][i]/(double)stepm; 
   } /* End age */          /* bias bh is positive if real duration
             * is higher than the multiple of stepm and negative otherwise.
   free_vector(xp,1,npar);           */
   free_matrix(doldm,1,nlstate,1,npar);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   free_matrix(dnewm,1,nlstate,1,nlstate);          if( s2 > nlstate){ 
             /* i.e. if s2 is a death state and if the date of death is known 
 }               then the contribution to the likelihood is the probability to 
                die between last step unit time and current  step unit time, 
 /************ Variance of prevlim ******************/               which is also equal to probability to die before dh 
 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)               minus probability to die before dh-stepm . 
 {               In version up to 0.92 likelihood was computed
   /* Variance of prevalence limit */          as if date of death was unknown. Death was treated as any other
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          health state: the date of the interview describes the actual state
   double **newm;          and not the date of a change in health state. The former idea was
   double **dnewm,**doldm;          to consider that at each interview the state was recorded
   int i, j, nhstepm, hstepm;          (healthy, disable or death) and IMaCh was corrected; but when we
   int k, cptcode;          introduced the exact date of death then we should have modified
   double *xp;          the contribution of an exact death to the likelihood. This new
   double *gp, *gm;          contribution is smaller and very dependent of the step unit
   double **gradg, **trgradg;          stepm. It is no more the probability to die between last interview
   double age,agelim;          and month of death but the probability to survive from last
   int theta;          interview up to one month before death multiplied by the
              probability to die within a month. Thanks to Chris
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");          Jackson for correcting this bug.  Former versions increased
   fprintf(ficresvpl,"# Age");          mortality artificially. The bad side is that we add another loop
   for(i=1; i<=nlstate;i++)          which slows down the processing. The difference can be up to 10%
       fprintf(ficresvpl," %1d-%1d",i,i);          lower mortality.
   fprintf(ficresvpl,"\n");            */
             lli=log(out[s1][s2] - savm[s1][s2]);
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);          } else if  (s2==-2) {
              for (j=1,survp=0. ; j<=nlstate; j++) 
   hstepm=1*YEARM; /* Every year of age */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            /*survp += out[s1][j]; */
   agelim = AGESUP;            lli= log(survp);
   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;          else if  (s2==-4) { 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            for (j=3,survp=0. ; j<=nlstate; j++)  
     gradg=matrix(1,npar,1,nlstate);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     gp=vector(1,nlstate);            lli= log(survp); 
     gm=vector(1,nlstate);          } 
   
     for(theta=1; theta <=npar; theta++){          else if  (s2==-5) { 
       for(i=1; i<=npar; i++){ /* Computes gradient */            for (j=1,survp=0. ; j<=2; j++)  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       }            lli= log(survp); 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          } 
       for(i=1;i<=nlstate;i++)          
         gp[i] = prlim[i][i];          else{
                lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for(i=1; i<=npar; i++) /* Computes gradient */            /*  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 */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       for(i=1;i<=nlstate;i++)          /*if(lli ==000.0)*/
         gm[i] = prlim[i][i];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           ipmx +=1;
       for(i=1;i<=nlstate;i++)          sw += weight[i];
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     } /* End theta */        } /* end of wave */
       } /* end of individual */
     trgradg =matrix(1,nlstate,1,npar);    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(j=1; j<=nlstate;j++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(theta=1; theta <=npar; theta++)        for(mi=1; mi<= wav[i]-1; mi++){
         trgradg[j][theta]=gradg[theta][j];          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
     for(i=1;i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       varpl[i][(int)age] =0.;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          for(d=0; d<=dh[mi][i]; d++){
     for(i=1;i<=nlstate;i++)            newm=savm;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     fprintf(ficresvpl,"%.0f ",age );              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(i=1; i<=nlstate;i++)            }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     fprintf(ficresvpl,"\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_vector(gp,1,nlstate);            savm=oldm;
     free_vector(gm,1,nlstate);            oldm=newm;
     free_matrix(gradg,1,npar,1,nlstate);          } /* end mult */
     free_matrix(trgradg,1,nlstate,1,npar);        
   } /* End age */          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   free_vector(xp,1,npar);          bbh=(double)bh[mi][i]/(double)stepm; 
   free_matrix(doldm,1,nlstate,1,npar);          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 */
   free_matrix(dnewm,1,nlstate,1,nlstate);          ipmx +=1;
           sw += weight[i];
 }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
 /************ Variance of one-step probabilities  ******************/      } /* end of individual */
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    }  else if(mle==3){  /* exponential inter-extrapolation */
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i, j=0,  i1, k1, l1, t, tj;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int k2, l2, j1,  z1;        for(mi=1; mi<= wav[i]-1; mi++){
   int k=0,l, cptcode;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int first=1;            for (j=1;j<=nlstate+ndeath;j++){
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **dnewm,**doldm;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *xp;            }
   double *gp, *gm;          for(d=0; d<dh[mi][i]; d++){
   double **gradg, **trgradg;            newm=savm;
   double **mu;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double age,agelim, cov[NCOVMAX];            for (kk=1; kk<=cptcovage;kk++) {
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int theta;            }
   char fileresprob[FILENAMELENGTH];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   char fileresprobcov[FILENAMELENGTH];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   char fileresprobcor[FILENAMELENGTH];            savm=oldm;
             oldm=newm;
   double ***varpij;          } /* end mult */
         
   strcpy(fileresprob,"prob");          s1=s[mw[mi][i]][i];
   strcat(fileresprob,fileres);          s2=s[mw[mi+1][i]][i];
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          bbh=(double)bh[mi][i]/(double)stepm; 
     printf("Problem with resultfile: %s\n", fileresprob);          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   }          ipmx +=1;
   strcpy(fileresprobcov,"probcov");          sw += weight[i];
   strcat(fileresprobcov,fileres);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {        } /* end of wave */
     printf("Problem with resultfile: %s\n", fileresprobcov);      } /* end of individual */
   }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   strcpy(fileresprobcor,"probcor");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcat(fileresprobcor,fileres);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {        for(mi=1; mi<= wav[i]-1; mi++){
     printf("Problem with resultfile: %s\n", fileresprobcor);          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);            }
            for(d=0; d<dh[mi][i]; d++){
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");            newm=savm;
   fprintf(ficresprob,"# Age");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");            for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficresprobcov,"# Age");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");            }
   fprintf(ficresprobcov,"# Age");          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for(i=1; i<=nlstate;i++)            savm=oldm;
     for(j=1; j<=(nlstate+ndeath);j++){            oldm=newm;
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);          } /* end mult */
       fprintf(ficresprobcov," p%1d-%1d ",i,j);        
       fprintf(ficresprobcor," p%1d-%1d ",i,j);          s1=s[mw[mi][i]][i];
     }            s2=s[mw[mi+1][i]][i];
   fprintf(ficresprob,"\n");          if( s2 > nlstate){ 
   fprintf(ficresprobcov,"\n");            lli=log(out[s1][s2] - savm[s1][s2]);
   fprintf(ficresprobcor,"\n");          }else{
   xp=vector(1,npar);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);          }
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));          ipmx +=1;
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);          sw += weight[i];
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   first=1;  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        } /* end of wave */
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);      } /* end of individual */
     exit(0);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   else{        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fprintf(ficgp,"\n# Routine varprob");        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {            for (j=1;j<=nlstate+ndeath;j++){
     printf("Problem with html file: %s\n", optionfilehtm);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     exit(0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
   else{          for(d=0; d<dh[mi][i]; d++){
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");            newm=savm;
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix 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> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
           
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   cov[1]=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   tj=cptcoveff;            savm=oldm;
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}            oldm=newm;
   j1=0;          } /* end mult */
   for(t=1; t<=tj;t++){        
     for(i1=1; i1<=ncodemax[t];i1++){          s1=s[mw[mi][i]][i];
       j1++;          s2=s[mw[mi+1][i]][i];
                lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       if  (cptcovn>0) {          ipmx +=1;
         fprintf(ficresprob, "\n#********** Variable ");          sw += weight[i];
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficresprob, "**********\n#");          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         fprintf(ficresprobcov, "\n#********** Variable ");        } /* end of wave */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      } /* end of individual */
         fprintf(ficresprobcov, "**********\n#");    } /* End of if */
            for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         fprintf(ficgp, "\n#********** Variable ");    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         fprintf(ficgp, "**********\n#");    return -l;
          }
          
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");  /*************** log-likelihood *************/
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  double funcone( double *x)
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");  {
            /* Same as likeli but slower because of a lot of printf and if */
         fprintf(ficresprobcor, "\n#********** Variable ");        int i, ii, j, k, mi, d, kk;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         fprintf(ficgp, "**********\n#");        double **out;
       }    double lli; /* Individual log likelihood */
          double llt;
       for (age=bage; age<=fage; age ++){    int s1, s2;
         cov[2]=age;    double bbh, survp;
         for (k=1; k<=cptcovn;k++) {    /*extern weight */
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    /* We are differentiating ll according to initial status */
         }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    /*for(i=1;i<imx;i++) 
         for (k=1; k<=cptcovprod;k++)      printf(" %d\n",s[4][i]);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    */
            cov[1]=1.;
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));  
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    for(k=1; k<=nlstate; k++) ll[k]=0.;
         gp=vector(1,(nlstate)*(nlstate+ndeath));  
         gm=vector(1,(nlstate)*(nlstate+ndeath));    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(theta=1; theta <=npar; theta++){      for(mi=1; mi<= wav[i]-1; mi++){
           for(i=1; i<=npar; i++)        for (ii=1;ii<=nlstate+ndeath;ii++)
             xp[i] = x[i] + (i==theta ?delti[theta]:0);          for (j=1;j<=nlstate+ndeath;j++){
                      oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                    }
           k=0;        for(d=0; d<dh[mi][i]; d++){
           for(i=1; i<= (nlstate); i++){          newm=savm;
             for(j=1; j<=(nlstate+ndeath);j++){          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               k=k+1;          for (kk=1; kk<=cptcovage;kk++) {
               gp[k]=pmmij[i][j];            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }          }
           }          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
                    out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           for(i=1; i<=npar; i++)                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             xp[i] = x[i] - (i==theta ?delti[theta]:0);          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
              /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          savm=oldm;
           k=0;          oldm=newm;
           for(i=1; i<=(nlstate); i++){        } /* end mult */
             for(j=1; j<=(nlstate+ndeath);j++){        
               k=k+1;        s1=s[mw[mi][i]][i];
               gm[k]=pmmij[i][j];        s2=s[mw[mi+1][i]][i];
             }        bbh=(double)bh[mi][i]/(double)stepm; 
           }        /* bias is positive if real duration
               * is higher than the multiple of stepm and negative otherwise.
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)         */
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          if( s2 > nlstate && (mle <5) ){  /* Jackson */
         }          lli=log(out[s1][s2] - savm[s1][s2]);
         } else if  (s2==-2) {
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)          for (j=1,survp=0. ; j<=nlstate; j++) 
           for(theta=1; theta <=npar; theta++)            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             trgradg[j][theta]=gradg[theta][j];          lli= log(survp);
                }else if (mle==1){
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);        } 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 */
         pmij(pmmij,cov,ncovmodel,x,nlstate);        } else if(mle==3){  /* exponential inter-extrapolation */
                  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 */
         k=0;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         for(i=1; i<=(nlstate); i++){          lli=log(out[s1][s2]); /* Original formula */
           for(j=1; j<=(nlstate+ndeath);j++){        } else{  /* mle=0 back to 1 */
             k=k+1;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             mu[k][(int) age]=pmmij[i][j];          /*lli=log(out[s1][s2]); */ /* Original formula */
           }        } /* End of if */
         }        ipmx +=1;
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)        sw += weight[i];
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             varpij[i][j][(int)age] = doldm[i][j];        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         if(globpr){
         /*printf("\n%d ",(int)age);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){   %11.6f %11.6f %11.6f ", \
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
      }*/                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         fprintf(ficresprob,"\n%d ",(int)age);            llt +=ll[k]*gipmx/gsw;
         fprintf(ficresprobcov,"\n%d ",(int)age);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         fprintf(ficresprobcor,"\n%d ",(int)age);          }
           fprintf(ficresilk," %10.6f\n", -llt);
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)        }
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));      } /* end of wave */
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    } /* end of individual */
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);    /* 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 */
         i=0;    if(globpr==0){ /* First time we count the contributions and weights */
         for (k=1; k<=(nlstate);k++){      gipmx=ipmx;
           for (l=1; l<=(nlstate+ndeath);l++){      gsw=sw;
             i=i++;    }
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    return -l;
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);  }
             for (j=1; j<=i;j++){  
               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]));  /*************** function likelione ***********/
             }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
           }  {
         }/* end of loop for state */    /* This routine should help understanding what is done with 
       } /* end of loop for age */       the selection of individuals/waves and
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/       to check the exact contribution to the likelihood.
       for (k1=1; k1<=(nlstate);k1++){       Plotting could be done.
         for (l1=1; l1<=(nlstate+ndeath);l1++){     */
           if(l1==k1) continue;    int k;
           i=(k1-1)*(nlstate+ndeath)+l1;  
           for (k2=1; k2<=(nlstate);k2++){    if(*globpri !=0){ /* Just counts and sums, no printings */
             for (l2=1; l2<=(nlstate+ndeath);l2++){      strcpy(fileresilk,"ilk"); 
               if(l2==k2) continue;      strcat(fileresilk,fileres);
               j=(k2-1)*(nlstate+ndeath)+l2;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
               if(j<=i) continue;        printf("Problem with resultfile: %s\n", fileresilk);
               for (age=bage; age<=fage; age ++){        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
                 if ((int)age %5==0){      }
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;      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");
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
                   mu1=mu[i][(int) age]/stepm*YEARM ;      for(k=1; k<=nlstate; k++) 
                   mu2=mu[j][(int) age]/stepm*YEARM;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
                   /* Computing eigen value of matrix of covariance */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    }
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));  
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);    *fretone=(*funcone)(p);
                   /* Eigen vectors */    if(*globpri !=0){
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));      fclose(ficresilk);
                   v21=sqrt(1.-v11*v11);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
                   v12=-v21;      fflush(fichtm); 
                   v22=v11;    } 
                   /*printf(fignu*/    return;
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */  }
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */  
                   if(first==1){  
                     first=0;  /*********** Maximum Likelihood Estimation ***************/
                     fprintf(ficgp,"\nset parametric;set nolabel");  
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");  {
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);    int i,j, iter=0;
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);    double **xi;
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);    double fret;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    double fretone; /* Only one call to likelihood */
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    /*  char filerespow[FILENAMELENGTH];*/
                     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)) t \"%d\"",\  
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \  #ifdef NLOPT
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    int creturn;
                   }else{    nlopt_opt opt;
                     first=0;    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    double *lb;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    double minf; /* the minimum objective value, upon return */
                     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)) t \"%d\"",\    double * p1; /* Shifted parameters from 0 instead of 1 */
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    myfunc_data dinst, *d = &dinst;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);  #endif
                   }/* if first */  
                 } /* age mod 5 */  
               } /* end loop age */    xi=matrix(1,npar,1,npar);
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);    for (i=1;i<=npar;i++)
               first=1;      for (j=1;j<=npar;j++)
             } /*l12 */        xi[i][j]=(i==j ? 1.0 : 0.0);
           } /* k12 */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         } /*l1 */    strcpy(filerespow,"pow"); 
       }/* k1 */    strcat(filerespow,fileres);
     } /* loop covariates */    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);      printf("Problem with resultfile: %s\n", filerespow);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    }
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for (i=1;i<=nlstate;i++)
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for(j=1;j<=nlstate+ndeath;j++)
   }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   free_vector(xp,1,npar);    fprintf(ficrespow,"\n");
   fclose(ficresprob);  #ifdef POWELL
   fclose(ficresprobcov);    powell(p,xi,npar,ftol,&iter,&fret,func);
   fclose(ficresprobcor);  #endif
   fclose(ficgp);  
   fclose(fichtm);  #ifdef NLOPT
 }  #ifdef NEWUOA
     opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   #else
 /******************* Printing html file ***********/    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  #endif
                   int lastpass, int stepm, int weightopt, char model[],\    lb=vector(0,npar-1);
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
                   int popforecast, int estepm ,\    nlopt_set_lower_bounds(opt, lb);
                   double jprev1, double mprev1,double anprev1, \    nlopt_set_initial_step1(opt, 0.1);
                   double jprev2, double mprev2,double anprev2){    
   int jj1, k1, i1, cpt;    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   /*char optionfilehtm[FILENAMELENGTH];*/    d->function = func;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     printf("Problem with %s \n",optionfilehtm), exit(0);    nlopt_set_min_objective(opt, myfunc, d);
   }    nlopt_set_xtol_rel(opt, ftol);
     if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n      printf("nlopt failed! %d\n",creturn); 
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n    }
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    else {
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
  - Life expectancies by age and initial health status (estepm=%2d months):      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
    <a href=\"e%s\">e%s</a> <br>\n</li>", \      iter=1; /* not equal */
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    }
     nlopt_destroy(opt);
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n  #endif
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    free_matrix(xi,1,npar,1,npar);
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    fclose(ficrespow);
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n  
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);  }
   
  if(popforecast==1) fprintf(fichtm,"\n  /**** Computes Hessian and covariance matrix ***/
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  {
         <br>",fileres,fileres,fileres,fileres);    double  **a,**y,*x,pd;
  else    double **hess;
    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);    int i, j;
 fprintf(fichtm," <li><b>Graphs</b></li><p>");    int *indx;
   
  m=cptcoveff;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     void lubksb(double **a, int npar, int *indx, double b[]) ;
  jj1=0;    void ludcmp(double **a, int npar, int *indx, double *d) ;
  for(k1=1; k1<=m;k1++){    double gompertz(double p[]);
    for(i1=1; i1<=ncodemax[k1];i1++){    hess=matrix(1,npar,1,npar);
      jj1++;  
      if (cptcovn > 0) {    printf("\nCalculation of the hessian matrix. Wait...\n");
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
        for (cpt=1; cpt<=cptcoveff;cpt++)    for (i=1;i<=npar;i++){
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      printf("%d",i);fflush(stdout);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      fprintf(ficlog,"%d",i);fflush(ficlog);
      }     
      /* Pij */       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>      
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          /*  printf(" %f ",p[i]);
      /* Quasi-incidences */          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>    }
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    
        /* Stable prevalence in each health state */    for (i=1;i<=npar;i++) {
        for(cpt=1; cpt<nlstate;cpt++){      for (j=1;j<=npar;j++)  {
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>        if (j>i) { 
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          printf(".%d%d",i,j);fflush(stdout);
        }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     for(cpt=1; cpt<=nlstate;cpt++) {          hess[i][j]=hessij(p,delti,i,j,func,npar);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          
 interval) in state (%d): v%s%d%d.png <br>          hess[j][i]=hess[i][j];    
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            /*printf(" %lf ",hess[i][j]);*/
      }        }
      for(cpt=1; cpt<=nlstate;cpt++) {      }
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    }
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    printf("\n");
      }    fprintf(ficlog,"\n");
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.png<br>    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
    }    
  }    a=matrix(1,npar,1,npar);
 fclose(fichtm);    y=matrix(1,npar,1,npar);
 }    x=vector(1,npar);
     indx=ivector(1,npar);
 /******************* Gnuplot file **************/    for (i=1;i<=npar;i++)
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;  
   int ng;    for (j=1;j<=npar;j++) {
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {      for (i=1;i<=npar;i++) x[i]=0;
     printf("Problem with file %s",optionfilegnuplot);      x[j]=1;
   }      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
 #ifdef windows        matcov[i][j]=x[i];
     fprintf(ficgp,"cd \"%s\" \n",pathc);      }
 #endif    }
 m=pow(2,cptcoveff);  
      printf("\n#Hessian matrix#\n");
  /* 1eme*/    fprintf(ficlog,"\n#Hessian matrix#\n");
   for (cpt=1; cpt<= nlstate ; cpt ++) {    for (i=1;i<=npar;i++) { 
    for (k1=1; k1<= m ; k1 ++) {      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
 #ifdef windows        fprintf(ficlog,"%.3e ",hess[i][j]);
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      }
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);      printf("\n");
 #endif      fprintf(ficlog,"\n");
 #ifdef unix    }
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    /* Recompute Inverse */
 #endif    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 for (i=1; i<= nlstate ; i ++) {    ludcmp(a,npar,indx,&pd);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /*  printf("\n#Hessian matrix recomputed#\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);    for (j=1;j<=npar;j++) {
     for (i=1; i<= nlstate ; i ++) {      for (i=1;i<=npar;i++) x[i]=0;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      x[j]=1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      lubksb(a,npar,indx,x);
 }      for (i=1;i<=npar;i++){ 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        y[i][j]=x[i];
      for (i=1; i<= nlstate ; i ++) {        printf("%.3e ",y[i][j]);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        fprintf(ficlog,"%.3e ",y[i][j]);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      }
 }        printf("\n");
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      fprintf(ficlog,"\n");
 #ifdef unix    }
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");    */
 #endif  
    }    free_matrix(a,1,npar,1,npar);
   }    free_matrix(y,1,npar,1,npar);
   /*2 eme*/    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
   for (k1=1; k1<= m ; k1 ++) {    free_matrix(hess,1,npar,1,npar);
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);  
      }
     for (i=1; i<= nlstate+1 ; i ++) {  
       k=2*i;  /*************** hessian matrix ****************/
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       for (j=1; j<= nlstate+1 ; j ++) {  {
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int i;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int l=1, lmax=20;
 }      double k1,k2;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    double p2[MAXPARM+1]; /* identical to x */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    double res;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       for (j=1; j<= nlstate+1 ; j ++) {    double fx;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int k=0,kmax=10;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    double l1;
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");    fx=func(x);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    for (i=1;i<=npar;i++) p2[i]=x[i];
       for (j=1; j<= nlstate+1 ; j ++) {    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      l1=pow(10,l);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      delts=delt;
 }        for(k=1 ; k <kmax; k=k+1){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        delt = delta*(l1*k);
       else fprintf(ficgp,"\" t\"\" w l 0,");        p2[theta]=x[theta] +delt;
     }        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
   }        p2[theta]=x[theta]-delt;
          k2=func(p2)-fx;
   /*3eme*/        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   for (k1=1; k1<= m ; k1 ++) {        
     for (cpt=1; cpt<= nlstate ; cpt ++) {  #ifdef DEBUGHESS
       k=2+nlstate*(2*cpt-2);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);  #endif
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          k=kmax;
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          k=kmax; l=lmax*10;
         }
 */        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       for (i=1; i< nlstate ; i ++) {          delts=delt;
         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);        }
       }
       }    }
     }    delti[theta]=delts;
   }    return res; 
      
   /* CV preval stat */  }
     for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
       k=3;  {
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    int i;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    int l=1, lmax=20;
     double k1,k2,k3,k4,res,fx;
       for (i=1; i< nlstate ; i ++)    double p2[MAXPARM+1];
         fprintf(ficgp,"+$%d",k+i+1);    int k;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);  
          fx=func(x);
       l=3+(nlstate+ndeath)*cpt;    for (k=1; k<=2; k++) {
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      for (i=1;i<=npar;i++) p2[i]=x[i];
       for (i=1; i< nlstate ; i ++) {      p2[thetai]=x[thetai]+delti[thetai]/k;
         l=3+(nlstate+ndeath)*cpt;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         fprintf(ficgp,"+$%d",l+i+1);      k1=func(p2)-fx;
       }    
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        p2[thetai]=x[thetai]+delti[thetai]/k;
     }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   }        k2=func(p2)-fx;
      
   /* proba elementaires */      p2[thetai]=x[thetai]-delti[thetai]/k;
    for(i=1,jk=1; i <=nlstate; i++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     for(k=1; k <=(nlstate+ndeath); k++){      k3=func(p2)-fx;
       if (k != i) {    
         for(j=1; j <=ncovmodel; j++){      p2[thetai]=x[thetai]-delti[thetai]/k;
              p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      k4=func(p2)-fx;
           jk++;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
           fprintf(ficgp,"\n");  #ifdef DEBUG
         }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       }      fprintf(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);
     }  #endif
    }    }
     return res;
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/  }
      for(jk=1; jk <=m; jk++) {  
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);  /************** Inverse of matrix **************/
        if (ng==2)  void ludcmp(double **a, int n, int *indx, double *d) 
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");  { 
        else    int i,imax,j,k; 
          fprintf(ficgp,"\nset title \"Probability\"\n");    double big,dum,sum,temp; 
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    double *vv; 
        i=1;   
        for(k2=1; k2<=nlstate; k2++) {    vv=vector(1,n); 
          k3=i;    *d=1.0; 
          for(k=1; k<=(nlstate+ndeath); k++) {    for (i=1;i<=n;i++) { 
            if (k != k2){      big=0.0; 
              if(ng==2)      for (j=1;j<=n;j++) 
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);        if ((temp=fabs(a[i][j])) > big) big=temp; 
              else      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      vv[i]=1.0/big; 
              ij=1;    } 
              for(j=3; j <=ncovmodel; j++) {    for (j=1;j<=n;j++) { 
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      for (i=1;i<j;i++) { 
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        sum=a[i][j]; 
                  ij++;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
                }        a[i][j]=sum; 
                else      } 
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      big=0.0; 
              }      for (i=j;i<=n;i++) { 
              fprintf(ficgp,")/(1");        sum=a[i][j]; 
                      for (k=1;k<j;k++) 
              for(k1=1; k1 <=nlstate; k1++){            sum -= a[i][k]*a[k][j]; 
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        a[i][j]=sum; 
                ij=1;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
                for(j=3; j <=ncovmodel; j++){          big=dum; 
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          imax=i; 
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        } 
                    ij++;      } 
                  }      if (j != imax) { 
                  else        for (k=1;k<=n;k++) { 
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          dum=a[imax][k]; 
                }          a[imax][k]=a[j][k]; 
                fprintf(ficgp,")");          a[j][k]=dum; 
              }        } 
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);        *d = -(*d); 
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        vv[imax]=vv[j]; 
              i=i+ncovmodel;      } 
            }      indx[j]=imax; 
          }      if (a[j][j] == 0.0) a[j][j]=TINY; 
        }      if (j != n) { 
      }        dum=1.0/(a[j][j]); 
    }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
    fclose(ficgp);      } 
 }  /* end gnuplot */    } 
     free_vector(vv,1,n);  /* Doesn't work */
   ;
 /*************** Moving average **************/  } 
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){  
   void lubksb(double **a, int n, int *indx, double b[]) 
   int i, cpt, cptcod;  { 
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    int i,ii=0,ip,j; 
       for (i=1; i<=nlstate;i++)    double sum; 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)   
           mobaverage[(int)agedeb][i][cptcod]=0.;    for (i=1;i<=n;i++) { 
          ip=indx[i]; 
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){      sum=b[ip]; 
       for (i=1; i<=nlstate;i++){      b[ip]=b[i]; 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      if (ii) 
           for (cpt=0;cpt<=4;cpt++){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      else if (sum) ii=i; 
           }      b[i]=sum; 
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    } 
         }    for (i=n;i>=1;i--) { 
       }      sum=b[i]; 
     }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
          b[i]=sum/a[i][i]; 
 }    } 
   } 
   
 /************** Forecasting ******************/  void pstamp(FILE *fichier)
 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){  {
      fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  }
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  /************ Frequencies ********************/
   double *popeffectif,*popcount;  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[])
   double ***p3mat;  {  /* Some frequencies */
   char fileresf[FILENAMELENGTH];    
     int i, m, jk, j1, bool, z1,j;
  agelim=AGESUP;    int first;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    double ***freq; /* Frequencies */
     double *pp, **prop;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
      char fileresp[FILENAMELENGTH];
      
   strcpy(fileresf,"f");    pp=vector(1,nlstate);
   strcat(fileresf,fileres);    prop=matrix(1,nlstate,iagemin,iagemax+3);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    strcpy(fileresp,"p");
     printf("Problem with forecast resultfile: %s\n", fileresf);    strcat(fileresp,fileres);
   }    if((ficresp=fopen(fileresp,"w"))==NULL) {
   printf("Computing forecasting: result on file '%s' \n", fileresf);      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      exit(0);
     }
   if (mobilav==1) {    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    j1=0;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    
   }    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;    first=1;
    
   agelim=AGESUP;    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
      /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
   hstepm=1;    /*    j1++; */
   hstepm=hstepm/stepm;    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
   yp1=modf(dateintmean,&yp);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   anprojmean=yp;          scanf("%d", i);*/
   yp2=modf((yp1*12),&yp);        for (i=-5; i<=nlstate+ndeath; i++)  
   mprojmean=yp;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
   yp1=modf((yp2*30.5),&yp);            for(m=iagemin; m <= iagemax+3; m++)
   jprojmean=yp;              freq[i][jk][m]=0;
   if(jprojmean==0) jprojmean=1;        
   if(mprojmean==0) jprojmean=1;        for (i=1; i<=nlstate; i++)  
            for(m=iagemin; m <= iagemax+3; m++)
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);            prop[i][m]=0;
          
   for(cptcov=1;cptcov<=i2;cptcov++){        dateintsum=0;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        k2cpt=0;
       k=k+1;        for (i=1; i<=imx; i++) {
       fprintf(ficresf,"\n#******");          bool=1;
       for(j=1;j<=cptcoveff;j++) {          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for (z1=1; z1<=cptcoveff; z1++)       
       }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
       fprintf(ficresf,"******\n");                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
       fprintf(ficresf,"# StartingAge FinalAge");                bool=0;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
                        bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
                        j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
         fprintf(ficresf,"\n");              } 
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            }
    
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          if (bool==1){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            for(m=firstpass; m<=lastpass; m++){
           nhstepm = nhstepm/hstepm;              k2=anint[m][i]+(mint[m][i]/12.);
                        /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           oldm=oldms;savm=savms;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                        if (m<lastpass) {
           for (h=0; h<=nhstepm; h++){                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
             if (h==(int) (calagedate+YEARM*cpt)) {                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);                }
             }                
             for(j=1; j<=nlstate+ndeath;j++) {                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
               kk1=0.;kk2=0;                  dateintsum=dateintsum+k2;
               for(i=1; i<=nlstate;i++) {                                k2cpt++;
                 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];          }
                 }        } /* end i */
                         
               }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
               if (h==(int)(calagedate+12*cpt)){        pstamp(ficresp);
                 fprintf(ficresf," %.3f", kk1);        if  (cptcovn>0) {
                                  fprintf(ficresp, "\n#********** Variable "); 
               }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             }          fprintf(ficresp, "**********\n#");
           }          fprintf(ficlog, "\n#********** Variable "); 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         }          fprintf(ficlog, "**********\n#");
       }        }
     }        for(i=1; i<=nlstate;i++) 
   }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
                fprintf(ficresp, "\n");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        
         for(i=iagemin; i <= iagemax+3; i++){
   fclose(ficresf);          if(i==iagemax+3){
 }            fprintf(ficlog,"Total");
 /************** Forecasting ******************/          }else{
 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){            if(first==1){
                first=0;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              printf("See log file for details...\n");
   int *popage;            }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            fprintf(ficlog,"Age %d", i);
   double *popeffectif,*popcount;          }
   double ***p3mat,***tabpop,***tabpopprev;          for(jk=1; jk <=nlstate ; jk++){
   char filerespop[FILENAMELENGTH];            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(jk=1; jk <=nlstate ; jk++){
   agelim=AGESUP;            for(m=-1, pos=0; m <=0 ; m++)
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;              pos += freq[jk][m][i];
              if(pp[jk]>=1.e-10){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              if(first==1){
                  printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                }
   strcpy(filerespop,"pop");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   strcat(filerespop,fileres);            }else{
   if((ficrespop=fopen(filerespop,"w"))==NULL) {              if(first==1)
     printf("Problem with forecast resultfile: %s\n", filerespop);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   printf("Computing forecasting: result on file '%s' \n", filerespop);            }
           }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
           for(jk=1; jk <=nlstate ; jk++){
   if (mobilav==1) {            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              pp[jk] += freq[jk][m][i];
     movingaverage(agedeb, fage, ageminpar, mobaverage);          }       
   }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
   stepsize=(int) (stepm+YEARM-1)/YEARM;            posprop += prop[jk][i];
   if (stepm<=12) stepsize=1;          }
            for(jk=1; jk <=nlstate ; jk++){
   agelim=AGESUP;            if(pos>=1.e-5){
                if(first==1)
   hstepm=1;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   hstepm=hstepm/stepm;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
              }else{
   if (popforecast==1) {              if(first==1)
     if((ficpop=fopen(popfile,"r"))==NULL) {                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       printf("Problem with population file : %s\n",popfile);exit(0);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     }            }
     popage=ivector(0,AGESUP);            if( i <= iagemax){
     popeffectif=vector(0,AGESUP);              if(pos>=1.e-5){
     popcount=vector(0,AGESUP);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                    /*probs[i][jk][j1]= pp[jk]/pos;*/
     i=1;                  /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;              }
                  else
     imx=i;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            }
   }          }
           
   for(cptcov=1;cptcov<=i2;cptcov++){          for(jk=-1; jk <=nlstate+ndeath; jk++)
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            for(m=-1; m <=nlstate+ndeath; m++)
       k=k+1;              if(freq[jk][m][i] !=0 ) {
       fprintf(ficrespop,"\n#******");              if(first==1)
       for(j=1;j<=cptcoveff;j++) {                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       }              }
       fprintf(ficrespop,"******\n");          if(i <= iagemax)
       fprintf(ficrespop,"# Age");            fprintf(ficresp,"\n");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          if(first==1)
       if (popforecast==1)  fprintf(ficrespop," [Population]");            printf("Others in log...\n");
                fprintf(ficlog,"\n");
       for (cpt=0; cpt<=0;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--){    dateintmean=dateintsum/k2cpt; 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);   
           nhstepm = nhstepm/hstepm;    fclose(ficresp);
              free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_vector(pp,1,nlstate);
           oldm=oldms;savm=savms;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /* End of Freq */
          }
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {  /************ Prevalence ********************/
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  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)
             }  {  
             for(j=1; j<=nlstate+ndeath;j++) {    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
               kk1=0.;kk2=0;       in each health status at the date of interview (if between dateprev1 and dateprev2).
               for(i=1; i<=nlstate;i++) {                     We still use firstpass and lastpass as another selection.
                 if (mobilav==1)    */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];   
                 else {    int i, m, jk, j1, bool, z1,j;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }    double **prop;
               }    double posprop; 
               if (h==(int)(calagedate+12*cpt)){    double  y2; /* in fractional years */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    int iagemin, iagemax;
                   /*fprintf(ficrespop," %.3f", kk1);    int first; /** to stop verbosity which is redirected to log file */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }    iagemin= (int) agemin;
             }    iagemax= (int) agemax;
             for(i=1; i<=nlstate;i++){    /*pp=vector(1,nlstate);*/
               kk1=0.;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
                 for(j=1; j<=nlstate;j++){    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    j1=0;
                 }    
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    /*j=cptcoveff;*/
             }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    first=1;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
           }      /*for(i1=1; i1<=ncodemax[k1];i1++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        j1++;*/
         }        
       }        for (i=1; i<=nlstate; i++)  
            for(m=iagemin; m <= iagemax+3; m++)
   /******/            prop[i][m]=0.0;
        
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        for (i=1; i<=imx; i++) { /* Each individual */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            bool=1;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          if  (cptcovn>0) {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            for (z1=1; z1<=cptcoveff; z1++) 
           nhstepm = nhstepm/hstepm;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                          bool=0;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          } 
           oldm=oldms;savm=savms;          if (bool==1) { 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           for (h=0; h<=nhstepm; h++){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
             if (h==(int) (calagedate+YEARM*cpt)) {              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             for(j=1; j<=nlstate+ndeath;j++) {                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); 
               kk1=0.;kk2=0;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
               for(i=1; i<=nlstate;i++) {                                /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                      prop[s[m][i]][(int)agev[m][i]] += weight[i];
               }                  prop[s[m][i]][iagemax+3] += weight[i]; 
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);                } 
             }              }
           }            } /* end selection of waves */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
         }        }
       }        for(i=iagemin; i <= iagemax+3; i++){  
    }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   }            posprop += prop[jk][i]; 
            } 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          
           for(jk=1; jk <=nlstate ; jk++){     
   if (popforecast==1) {            if( i <=  iagemax){ 
     free_ivector(popage,0,AGESUP);              if(posprop>=1.e-5){ 
     free_vector(popeffectif,0,AGESUP);                probs[i][jk][j1]= prop[jk][i]/posprop;
     free_vector(popcount,0,AGESUP);              } else{
   }                if(first==1){
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                  first=0;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                  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]);
   fclose(ficrespop);                }
 }              }
             } 
 /***********************************************/          }/* end jk */ 
 /**************** Main Program *****************/        }/* end i */ 
 /***********************************************/      /*} *//* end i1 */
     } /* end j1 */
 int main(int argc, char *argv[])    
 {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   double agedeb, agefin,hf;  }  /* End of prevalence */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  
   /************* Waves Concatenation ***************/
   double fret;  
   double **xi,tmp,delta;  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)
   {
   double dum; /* Dummy variable */    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   double ***p3mat;       Death is a valid wave (if date is known).
   int *indx;       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   char line[MAXLINE], linepar[MAXLINE];       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];       and mw[mi+1][i]. dh depends on stepm.
   int firstobs=1, lastobs=10;       */
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;    int i, mi, m;
   int ju,jl, mi;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;       double sum=0., jmean=0.;*/
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    int first;
   int mobilav=0,popforecast=0;    int j, k=0,jk, ju, jl;
   int hstepm, nhstepm;    double sum=0.;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    first=0;
     jmin=100000;
   double bage, fage, age, agelim, agebase;    jmax=-1;
   double ftolpl=FTOL;    jmean=0.;
   double **prlim;    for(i=1; i<=imx; i++){
   double *severity;      mi=0;
   double ***param; /* Matrix of parameters */      m=firstpass;
   double  *p;      while(s[m][i] <= nlstate){
   double **matcov; /* Matrix of covariance */        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   double ***delti3; /* Scale */          mw[++mi][i]=m;
   double *delti; /* Scale */        if(m >=lastpass)
   double ***eij, ***vareij;          break;
   double **varpl; /* Variances of prevalence limits by age */        else
   double *epj, vepp;          m++;
   double kk1, kk2;      }/* end while */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      if (s[m][i] > nlstate){
          mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
   char *alph[]={"a","a","b","c","d","e"}, str[4];           /* Only death is a correct wave */
         mw[mi][i]=m;
       }
   char z[1]="c", occ;  
 #include <sys/time.h>      wav[i]=mi;
 #include <time.h>      if(mi==0){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        nbwarn++;
          if(first==0){
   /* long total_usecs;          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   struct timeval start_time, end_time;          first=1;
          }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        if(first==1){
   getcwd(pathcd, size);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         }
   printf("\n%s",version);      } /* end mi==0 */
   if(argc <=1){    } /* End individuals */
     printf("\nEnter the parameter file name: ");  
     scanf("%s",pathtot);    for(i=1; i<=imx; i++){
   }      for(mi=1; mi<wav[i];mi++){
   else{        if (stepm <=0)
     strcpy(pathtot,argv[1]);          dh[mi][i]=1;
   }        else{
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   /*cygwin_split_path(pathtot,path,optionfile);            if (agedc[i] < 2*AGESUP) {
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   /* cutv(path,optionfile,pathtot,'\\');*/              if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);                nberr++;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                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]);
   chdir(path);                j=1; /* Temporary Dangerous patch */
   replace(pathc,path);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                 fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
 /*-------- arguments in the command line --------*/                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);
               }
   strcpy(fileres,"r");              k=k+1;
   strcat(fileres, optionfilefiname);              if (j >= jmax){
   strcat(fileres,".txt");    /* Other files have txt extension */                jmax=j;
                 ijmax=i;
   /*---------arguments file --------*/              }
               if (j <= jmin){
   if((ficpar=fopen(optionfile,"r"))==NULL)    {                jmin=j;
     printf("Problem with optionfile %s\n",optionfile);                ijmin=i;
     goto end;              }
   }              sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   strcpy(filereso,"o");              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   strcat(filereso,fileres);            }
   if((ficparo=fopen(filereso,"w"))==NULL) {          }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          else{
   }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){            k=k+1;
     ungetc(c,ficpar);            if (j >= jmax) {
     fgets(line, MAXLINE, ficpar);              jmax=j;
     puts(line);              ijmax=i;
     fputs(line,ficparo);            }
   }            else if (j <= jmin){
   ungetc(c,ficpar);              jmin=j;
               ijmin=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);            }
   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);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   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);            /*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]);*/
 while((c=getc(ficpar))=='#' && c!= EOF){            if(j<0){
     ungetc(c,ficpar);              nberr++;
     fgets(line, MAXLINE, ficpar);              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]);
     puts(line);              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]);
     fputs(line,ficparo);            }
   }            sum=sum+j;
   ungetc(c,ficpar);          }
            jk= j/stepm;
              jl= j -jk*stepm;
   covar=matrix(0,NCOVMAX,1,n);          ju= j -(jk+1)*stepm;
   cptcovn=0;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;            if(jl==0){
               dh[mi][i]=jk;
   ncovmodel=2+cptcovn;              bh[mi][i]=0;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */            }else{ /* We want a negative bias in order to only have interpolation ie
                      * to avoid the price of an extra matrix product in likelihood */
   /* Read guess parameters */              dh[mi][i]=jk+1;
   /* Reads comments: lines beginning with '#' */              bh[mi][i]=ju;
   while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);          }else{
     fgets(line, MAXLINE, ficpar);            if(jl <= -ju){
     puts(line);              dh[mi][i]=jk;
     fputs(line,ficparo);              bh[mi][i]=jl;       /* bias is positive if real duration
   }                                   * is higher than the multiple of stepm and negative otherwise.
   ungetc(c,ficpar);                                   */
              }
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            else{
     for(i=1; i <=nlstate; i++)              dh[mi][i]=jk+1;
     for(j=1; j <=nlstate+ndeath-1; j++){              bh[mi][i]=ju;
       fscanf(ficpar,"%1d%1d",&i1,&j1);            }
       fprintf(ficparo,"%1d%1d",i1,j1);            if(dh[mi][i]==0){
       printf("%1d%1d",i,j);              dh[mi][i]=1; /* At least one step */
       for(k=1; k<=ncovmodel;k++){              bh[mi][i]=ju; /* At least one step */
         fscanf(ficpar," %lf",&param[i][j][k]);              /*  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);*/
         printf(" %lf",param[i][j][k]);            }
         fprintf(ficparo," %lf",param[i][j][k]);          } /* end if mle */
       }        }
       fscanf(ficpar,"\n");      } /* end wave */
       printf("\n");    }
       fprintf(ficparo,"\n");    jmean=sum/k;
     }    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
      fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;   }
   
   p=param[1][1];  /*********** Tricode ****************************/
    void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   /* Reads comments: lines beginning with '#' */  {
   while((c=getc(ficpar))=='#' && c!= EOF){    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
     ungetc(c,ficpar);    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
     fgets(line, MAXLINE, ficpar);     * Boring subroutine which should only output nbcode[Tvar[j]][k]
     puts(line);     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
     fputs(line,ficparo);     * nbcode[Tvar[j]][1]= 
   }    */
   ungetc(c,ficpar);  
     int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    int modmaxcovj=0; /* Modality max of covariates j */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    int cptcode=0; /* Modality max of covariates j */
   for(i=1; i <=nlstate; i++){    int modmincovj=0; /* Modality min of covariates j */
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);    cptcoveff=0; 
       fprintf(ficparo,"%1d%1d",i1,j1);   
       for(k=1; k<=ncovmodel;k++){    for (k=-1; k < maxncov; k++) Ndum[k]=0;
         fscanf(ficpar,"%le",&delti3[i][j][k]);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
         printf(" %le",delti3[i][j][k]);  
         fprintf(ficparo," %le",delti3[i][j][k]);    /* Loop on covariates without age and products */
       }    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
       fscanf(ficpar,"\n");      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
       printf("\n");                                 modality of this covariate Vj*/ 
       fprintf(ficparo,"\n");        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
     }                                      * If product of Vn*Vm, still boolean *:
   }                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
   delti=delti3[1][1];                                      * 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
   /* Reads comments: lines beginning with '#' */                                        modality of the nth covariate of individual i. */
   while((c=getc(ficpar))=='#' && c!= EOF){        if (ij > modmaxcovj)
     ungetc(c,ficpar);          modmaxcovj=ij; 
     fgets(line, MAXLINE, ficpar);        else if (ij < modmincovj) 
     puts(line);          modmincovj=ij; 
     fputs(line,ficparo);        if ((ij < -1) && (ij > NCOVMAX)){
   }          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   ungetc(c,ficpar);          exit(1);
          }else
   matcov=matrix(1,npar,1,npar);        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
   for(i=1; i <=npar; i++){        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
     fscanf(ficpar,"%s",&str);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     printf("%s",str);        /* getting the maximum value of the modality of the covariate
     fprintf(ficparo,"%s",str);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
     for(j=1; j <=i; j++){           female is 1, then modmaxcovj=1.*/
       fscanf(ficpar," %le",&matcov[i][j]);      }
       printf(" %.5le",matcov[i][j]);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       fprintf(ficparo," %.5le",matcov[i][j]);      cptcode=modmaxcovj;
     }      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
     fscanf(ficpar,"\n");     /*for (i=0; i<=cptcode; i++) {*/
     printf("\n");      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
     fprintf(ficparo,"\n");        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
   }        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
   for(i=1; i <=npar; i++)          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
     for(j=i+1;j<=npar;j++)        }
       matcov[i][j]=matcov[j][i];        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
               historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
   printf("\n");      } /* Ndum[-1] number of undefined modalities */
   
       /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
     /*-------- Rewriting paramater file ----------*/      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
      strcpy(rfileres,"r");    /* "Rparameterfile */      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/         modmincovj=3; modmaxcovj = 7;
      strcat(rfileres,".");    /* */         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
      strcat(rfileres,optionfilext);    /* Other files have txt extension */         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
     if((ficres =fopen(rfileres,"w"))==NULL) {         variables V1_1 and V1_2.
       printf("Problem writing new parameter file: %s\n", fileres);goto end;         nbcode[Tvar[j]][ij]=k;
     }         nbcode[Tvar[j]][1]=0;
     fprintf(ficres,"#%s\n",version);         nbcode[Tvar[j]][2]=1;
             nbcode[Tvar[j]][3]=2;
     /*-------- data file ----------*/      */
     if((fic=fopen(datafile,"r"))==NULL)    {      ij=1; /* ij is similar to i but can jumps over null modalities */
       printf("Problem with datafile: %s\n", datafile);goto end;      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
     }        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
           /*recode from 0 */
     n= lastobs;          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
     severity = vector(1,maxwav);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
     outcome=imatrix(1,maxwav+1,1,n);                                       k is a modality. If we have model=V1+V1*sex 
     num=ivector(1,n);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     moisnais=vector(1,n);            ij++;
     annais=vector(1,n);          }
     moisdc=vector(1,n);          if (ij > ncodemax[j]) break; 
     andc=vector(1,n);        }  /* end of loop on */
     agedc=vector(1,n);      } /* end of loop on modality */ 
     cod=ivector(1,n);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     weight=vector(1,n);    
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
     mint=matrix(1,maxwav,1,n);    
     anint=matrix(1,maxwav,1,n);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
     s=imatrix(1,maxwav+1,1,n);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
     adl=imatrix(1,maxwav+1,1,n);         ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
     tab=ivector(1,NCOVMAX);     Ndum[ij]++; 
     ncodemax=ivector(1,8);   } 
   
     i=1;   ij=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
       if ((i >= firstobs) && (i <=lastobs)) {     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
             if((Ndum[i]!=0) && (i<=ncovcol)){
         for (j=maxwav;j>=1;j--){       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);       Tvaraff[ij]=i; /*For printing (unclear) */
           strcpy(line,stra);       ij++;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);     }else
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);         Tvaraff[ij]=0;
         }   }
           ij--;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);   cptcoveff=ij; /*Number of total covariates*/
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
   }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  
   /*********** Health Expectancies ****************/
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  
         for (j=ncovcol;j>=1;j--){  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }  {
         num[i]=atol(stra);    /* Health expectancies, no variances */
            int i, j, nhstepm, hstepm, h, nstepm;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    int nhstepma, nstepma; /* Decreasing with age */
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    double age, agelim, hf;
     double ***p3mat;
         i=i+1;    double eip;
       }  
     }    pstamp(ficreseij);
     /* printf("ii=%d", ij);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
        scanf("%d",i);*/    fprintf(ficreseij,"# Age");
   imx=i-1; /* Number of individuals */    for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
   /* for (i=1; i<=imx; i++){        fprintf(ficreseij," e%1d%1d ",i,j);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      }
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      fprintf(ficreseij," e%1d. ",i);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    }
     }*/    fprintf(ficreseij,"\n");
    /*  for (i=1; i<=imx; i++){  
      if (s[4][i]==9)  s[4][i]=-1;    
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
      }
   /* Calculation of the number of parameter from char model*/    else  hstepm=estepm;   
   Tvar=ivector(1,15);    /* We compute the life expectancy from trapezoids spaced every estepm months
   Tprod=ivector(1,15);     * This is mainly to measure the difference between two models: for example
   Tvaraff=ivector(1,15);     * if stepm=24 months pijx are given only every 2 years and by summing them
   Tvard=imatrix(1,15,1,2);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   Tage=ivector(1,15);           * progression in between and thus overestimating or underestimating according
         * to the curvature of the survival function. If, for the same date, we 
   if (strlen(model) >1){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     j=0, j1=0, k1=1, k2=1;     * to compare the new estimate of Life expectancy with the same linear 
     j=nbocc(model,'+');     * hypothesis. A more precise result, taking into account a more precise
     j1=nbocc(model,'*');     * curvature will be obtained if estepm is as small as stepm. */
     cptcovn=j+1;  
     cptcovprod=j1;    /* 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. 
     strcpy(modelsav,model);       nhstepm is the number of hstepm from age to agelim 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){       nstepm is the number of stepm from age to agelin. 
       printf("Error. Non available option model=%s ",model);       Look at hpijx to understand the reason of that which relies in memory size
       goto end;       and note for a fixed period like estepm months */
     }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           survival function given by stepm (the optimization length). Unfortunately it
     for(i=(j+1); i>=1;i--){       means that if the survival funtion is printed only each two years of age and if
       cutv(stra,strb,modelsav,'+');       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);       results. So we changed our mind and took the option of the best precision.
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    */
       /*scanf("%d",i);*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       if (strchr(strb,'*')) {  
         cutv(strd,strc,strb,'*');    agelim=AGESUP;
         if (strcmp(strc,"age")==0) {    /* If stepm=6 months */
           cptcovprod--;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           cutv(strb,stre,strd,'V');         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           Tvar[i]=atoi(stre);      
           cptcovage++;  /* nhstepm age range expressed in number of stepm */
             Tage[cptcovage]=i;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
             /*printf("stre=%s ", stre);*/    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         }    /* if (stepm >= YEARM) hstepm=1;*/
         else if (strcmp(strd,"age")==0) {    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           cptcovprod--;    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           cutv(strb,stre,strc,'V');  
           Tvar[i]=atoi(stre);    for (age=bage; age<=fage; age ++){ 
           cptcovage++;      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
           Tage[cptcovage]=i;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         }      /* if (stepm >= YEARM) hstepm=1;*/
         else {      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
           cutv(strb,stre,strc,'V');  
           Tvar[i]=ncovcol+k1;      /* If stepm=6 months */
           cutv(strb,strc,strd,'V');      /* Computed by stepm unit matrices, product of hstepma matrices, stored
           Tprod[k1]=i;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           Tvard[k1][1]=atoi(strc);      
           Tvard[k1][2]=atoi(stre);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
           Tvar[cptcovn+k2]=Tvard[k1][1];      
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           for (k=1; k<=lastobs;k++)      
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      printf("%d|",(int)age);fflush(stdout);
           k1++;      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           k2=k2+2;      
         }      /* Computing expectancies */
       }      for(i=1; i<=nlstate;i++)
       else {        for(j=1; j<=nlstate;j++)
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
        /*  scanf("%d",i);*/            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       cutv(strd,strc,strb,'V');            
       Tvar[i]=atoi(strc);            /* 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]);*/
       }  
       strcpy(modelsav,stra);            }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/      fprintf(ficreseij,"%3.0f",age );
     }      for(i=1; i<=nlstate;i++){
 }        eip=0;
          for(j=1; j<=nlstate;j++){
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          eip +=eij[i][j][(int)age];
   printf("cptcovprod=%d ", cptcovprod);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   scanf("%d ",i);*/        }
     fclose(fic);        fprintf(ficreseij,"%9.4f", eip );
       }
     /*  if(mle==1){*/      fprintf(ficreseij,"\n");
     if (weightopt != 1) { /* Maximisation without weights*/      
       for(i=1;i<=n;i++) weight[i]=1.0;    }
     }    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     /*-calculation of age at interview from date of interview and age at death -*/    printf("\n");
     agev=matrix(1,maxwav,1,imx);    fprintf(ficlog,"\n");
     
     for (i=1; i<=imx; i++) {  }
       for(m=2; (m<= maxwav); m++) {  
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  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[] )
          anint[m][i]=9999;  
          s[m][i]=-1;  {
        }    /* Covariances of health expectancies eij and of total life expectancies according
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;     to initial status i, ei. .
       }    */
     }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     int nhstepma, nstepma; /* Decreasing with age */
     for (i=1; i<=imx; i++)  {    double age, agelim, hf;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    double ***p3matp, ***p3matm, ***varhe;
       for(m=1; (m<= maxwav); m++){    double **dnewm,**doldm;
         if(s[m][i] >0){    double *xp, *xm;
           if (s[m][i] >= nlstate+1) {    double **gp, **gm;
             if(agedc[i]>0)    double ***gradg, ***trgradg;
               if(moisdc[i]!=99 && andc[i]!=9999)    int theta;
                 agev[m][i]=agedc[i];  
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    double eip, vip;
            else {  
               if (andc[i]!=9999){    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    xp=vector(1,npar);
               agev[m][i]=-1;    xm=vector(1,npar);
               }    dnewm=matrix(1,nlstate*nlstate,1,npar);
             }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
           }    
           else if(s[m][i] !=9){ /* Should no more exist */    pstamp(ficresstdeij);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
             if(mint[m][i]==99 || anint[m][i]==9999)    fprintf(ficresstdeij,"# Age");
               agev[m][i]=1;    for(i=1; i<=nlstate;i++){
             else if(agev[m][i] <agemin){      for(j=1; j<=nlstate;j++)
               agemin=agev[m][i];        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      fprintf(ficresstdeij," e%1d. ",i);
             }    }
             else if(agev[m][i] >agemax){    fprintf(ficresstdeij,"\n");
               agemax=agev[m][i];  
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    pstamp(ficrescveij);
             }    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
             /*agev[m][i]=anint[m][i]-annais[i];*/    fprintf(ficrescveij,"# Age");
             /*   agev[m][i] = age[i]+2*m;*/    for(i=1; i<=nlstate;i++)
           }      for(j=1; j<=nlstate;j++){
           else { /* =9 */        cptj= (j-1)*nlstate+i;
             agev[m][i]=1;        for(i2=1; i2<=nlstate;i2++)
             s[m][i]=-1;          for(j2=1; j2<=nlstate;j2++){
           }            cptj2= (j2-1)*nlstate+i2;
         }            if(cptj2 <= cptj)
         else /*= 0 Unknown */              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           agev[m][i]=1;          }
       }      }
        fprintf(ficrescveij,"\n");
     }    
     for (i=1; i<=imx; i++)  {    if(estepm < stepm){
       for(m=1; (m<= maxwav); m++){      printf ("Problem %d lower than %d\n",estepm, stepm);
         if (s[m][i] > (nlstate+ndeath)) {    }
           printf("Error: Wrong value in nlstate or ndeath\n");      else  hstepm=estepm;   
           goto end;    /* We compute the life expectancy from trapezoids spaced every estepm months
         }     * This is mainly to measure the difference between two models: for example
       }     * if stepm=24 months pijx are given only every 2 years and by summing them
     }     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);     * 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
     free_vector(severity,1,maxwav);     * to compare the new estimate of Life expectancy with the same linear 
     free_imatrix(outcome,1,maxwav+1,1,n);     * hypothesis. A more precise result, taking into account a more precise
     free_vector(moisnais,1,n);     * curvature will be obtained if estepm is as small as stepm. */
     free_vector(annais,1,n);  
     /* free_matrix(mint,1,maxwav,1,n);    /* For example we decided to compute the life expectancy with the smallest unit */
        free_matrix(anint,1,maxwav,1,n);*/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     free_vector(moisdc,1,n);       nhstepm is the number of hstepm from age to agelim 
     free_vector(andc,1,n);       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
           and note for a fixed period like estepm months */
     wav=ivector(1,imx);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     dh=imatrix(1,lastpass-firstpass+1,1,imx);       survival function given by stepm (the optimization length). Unfortunately it
     mw=imatrix(1,lastpass-firstpass+1,1,imx);       means that if the survival funtion is printed only each two years of age and if
           you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     /* Concatenates waves */       results. So we changed our mind and took the option of the best precision.
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
       Tcode=ivector(1,100);    /* If stepm=6 months */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    /* nhstepm age range expressed in number of stepm */
       ncodemax[1]=1;    agelim=AGESUP;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
          /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
    codtab=imatrix(1,100,1,10);    /* if (stepm >= YEARM) hstepm=1;*/
    h=0;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
    m=pow(2,cptcoveff);    
      p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    for(k=1;k<=cptcoveff; k++){    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      for(i=1; i <=(m/pow(2,k));i++){    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
        for(j=1; j <= ncodemax[k]; j++){    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    gp=matrix(0,nhstepm,1,nlstate*nlstate);
            h++;    gm=matrix(0,nhstepm,1,nlstate*nlstate);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;  
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    for (age=bage; age<=fage; age ++){ 
          }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
        }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      }      /* if (stepm >= YEARM) hstepm=1;*/
    }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);  
       codtab[1][2]=1;codtab[2][2]=2; */      /* If stepm=6 months */
    /* for(i=1; i <=m ;i++){      /* Computed by stepm unit matrices, product of hstepma matrices, stored
       for(k=1; k <=cptcovn; k++){         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);      
       }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       printf("\n");  
       }      /* Computing  Variances of health expectancies */
       scanf("%d",i);*/      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
             decrease memory allocation */
    /* Calculates basic frequencies. Computes observed prevalence at single age      for(theta=1; theta <=npar; theta++){
        and prints on file fileres'p'. */        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
              xm[i] = x[i] - (i==theta ?delti[theta]:0);
            }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1; j<= nlstate; j++){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          for(i=1; i<=nlstate; i++){
                  for(h=0; h<=nhstepm-1; h++){
     /* For Powell, parameters are in a vector p[] starting at p[1]              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            }
           }
     if(mle==1){        }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);       
     }        for(ij=1; ij<= nlstate*nlstate; ij++)
              for(h=0; h<=nhstepm-1; h++){
     /*--------- results files --------------*/            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
     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);          }
        }/* End theta */
       
    jk=1;      
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      for(h=0; h<=nhstepm-1; h++)
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        for(j=1; j<=nlstate*nlstate;j++)
    for(i=1,jk=1; i <=nlstate; i++){          for(theta=1; theta <=npar; theta++)
      for(k=1; k <=(nlstate+ndeath); k++){            trgradg[h][j][theta]=gradg[h][theta][j];
        if (k != i)      
          {  
            printf("%d%d ",i,k);       for(ij=1;ij<=nlstate*nlstate;ij++)
            fprintf(ficres,"%1d%1d ",i,k);        for(ji=1;ji<=nlstate*nlstate;ji++)
            for(j=1; j <=ncovmodel; j++){          varhe[ij][ji][(int)age] =0.;
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);       printf("%d|",(int)age);fflush(stdout);
              jk++;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
            }       for(h=0;h<=nhstepm-1;h++){
            printf("\n");        for(k=0;k<=nhstepm-1;k++){
            fprintf(ficres,"\n");          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
          }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
      }          for(ij=1;ij<=nlstate*nlstate;ij++)
    }            for(ji=1;ji<=nlstate*nlstate;ji++)
  if(mle==1){              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     /* Computing hessian and covariance matrix */        }
     ftolhess=ftol; /* Usually correct */      }
     hesscov(matcov, p, npar, delti, ftolhess, func);  
  }      /* Computing expectancies */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     printf("# Scales (for hessian or gradient estimation)\n");      for(i=1; i<=nlstate;i++)
      for(i=1,jk=1; i <=nlstate; i++){        for(j=1; j<=nlstate;j++)
       for(j=1; j <=nlstate+ndeath; j++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         if (j!=i) {            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
           fprintf(ficres,"%1d%1d",i,j);            
           printf("%1d%1d",i,j);            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
           for(k=1; k<=ncovmodel;k++){  
             printf(" %.5e",delti[jk]);          }
             fprintf(ficres," %.5e",delti[jk]);  
             jk++;      fprintf(ficresstdeij,"%3.0f",age );
           }      for(i=1; i<=nlstate;i++){
           printf("\n");        eip=0.;
           fprintf(ficres,"\n");        vip=0.;
         }        for(j=1; j<=nlstate;j++){
       }          eip += eij[i][j][(int)age];
      }          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
                vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
     k=1;          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
     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");        }
     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(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
     for(i=1;i<=npar;i++){      }
       /*  if (k>nlstate) k=1;      fprintf(ficresstdeij,"\n");
       i1=(i-1)/(ncovmodel*nlstate)+1;  
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      fprintf(ficrescveij,"%3.0f",age );
       printf("%s%d%d",alph[k],i1,tab[i]);*/      for(i=1; i<=nlstate;i++)
       fprintf(ficres,"%3d",i);        for(j=1; j<=nlstate;j++){
       printf("%3d",i);          cptj= (j-1)*nlstate+i;
       for(j=1; j<=i;j++){          for(i2=1; i2<=nlstate;i2++)
         fprintf(ficres," %.5e",matcov[i][j]);            for(j2=1; j2<=nlstate;j2++){
         printf(" %.5e",matcov[i][j]);              cptj2= (j2-1)*nlstate+i2;
       }              if(cptj2 <= cptj)
       fprintf(ficres,"\n");                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
       printf("\n");            }
       k++;        }
     }      fprintf(ficrescveij,"\n");
         
     while((c=getc(ficpar))=='#' && c!= EOF){    }
       ungetc(c,ficpar);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       fgets(line, MAXLINE, ficpar);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       puts(line);    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       fputs(line,ficparo);    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     }    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     ungetc(c,ficpar);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     estepm=0;    printf("\n");
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);    fprintf(ficlog,"\n");
     if (estepm==0 || estepm < stepm) estepm=stepm;  
     if (fage <= 2) {    free_vector(xm,1,npar);
       bage = ageminpar;    free_vector(xp,1,npar);
       fage = agemaxpar;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
        free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     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);  /************ 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[])
     while((c=getc(ficpar))=='#' && c!= EOF){  {
     ungetc(c,ficpar);    /* Variance of health expectancies */
     fgets(line, MAXLINE, ficpar);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     puts(line);    /* double **newm;*/
     fputs(line,ficparo);    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
   }    
   ungetc(c,ficpar);    int movingaverage();
      double **dnewm,**doldm;
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    double **dnewmp,**doldmp;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    int i, j, nhstepm, hstepm, h, nstepm ;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    int k;
          double *xp;
   while((c=getc(ficpar))=='#' && c!= EOF){    double **gp, **gm;  /* for var eij */
     ungetc(c,ficpar);    double ***gradg, ***trgradg; /*for var eij */
     fgets(line, MAXLINE, ficpar);    double **gradgp, **trgradgp; /* for var p point j */
     puts(line);    double *gpp, *gmp; /* for var p point j */
     fputs(line,ficparo);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   }    double ***p3mat;
   ungetc(c,ficpar);    double age,agelim, hf;
      double ***mobaverage;
     int theta;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    char digit[4];
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    char digitp[25];
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);    char fileresprobmorprev[FILENAMELENGTH];
   fprintf(ficparo,"pop_based=%d\n",popbased);    
   fprintf(ficres,"pop_based=%d\n",popbased);      if(popbased==1){
        if(mobilav!=0)
   while((c=getc(ficpar))=='#' && c!= EOF){        strcpy(digitp,"-populbased-mobilav-");
     ungetc(c,ficpar);      else strcpy(digitp,"-populbased-nomobil-");
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    else 
     fputs(line,ficparo);      strcpy(digitp,"-stablbased-");
   }  
   ungetc(c,ficpar);    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   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);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
 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(ficlog," Error in movingaverage mobilav=%d\n",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);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    strcpy(fileresprobmorprev,"prmorprev"); 
     fgets(line, MAXLINE, ficpar);    sprintf(digit,"%-d",ij);
     puts(line);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     fputs(line,ficparo);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   ungetc(c,ficpar);    strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 /*------------ gnuplot -------------*/    pstamp(ficresprobmorprev);
   strcpy(optionfilegnuplot,optionfilefiname);    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);
   strcat(optionfilegnuplot,".gp");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     printf("Problem with file %s",optionfilegnuplot);      fprintf(ficresprobmorprev," p.%-d SE",j);
   }      for(i=1; i<=nlstate;i++)
   fclose(ficgp);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    }  
 /*--------- index.htm --------*/    fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
   strcpy(optionfilehtm,optionfile);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   strcat(optionfilehtm,".htm");    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");
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     printf("Problem with %s \n",optionfilehtm), exit(0);  /*   } */
   }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    if(popbased==1)
 \n      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);
 Total number of observations=%d <br>\n    else
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
 <hr  size=\"2\" color=\"#EC5E5E\">    fprintf(ficresvij,"# Age");
  <ul><li><h4>Parameter files</h4>\n    for(i=1; i<=nlstate;i++)
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      for(j=1; j<=nlstate;j++)
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   fclose(fichtm);    fprintf(ficresvij,"\n");
   
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    xp=vector(1,npar);
      dnewm=matrix(1,nlstate,1,npar);
 /*------------ free_vector  -------------*/    doldm=matrix(1,nlstate,1,nlstate);
  chdir(path);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
      doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
  free_ivector(wav,1,imx);  
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      gpp=vector(nlstate+1,nlstate+ndeath);
  free_ivector(num,1,n);    gmp=vector(nlstate+1,nlstate+ndeath);
  free_vector(agedc,1,n);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    
  fclose(ficparo);    if(estepm < stepm){
  fclose(ficres);      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   /*--------------- Prevalence limit --------------*/    /* 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. 
   strcpy(filerespl,"pl");       nhstepm is the number of hstepm from age to agelim 
   strcat(filerespl,fileres);       nstepm is the number of stepm from age to agelin. 
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       Look at function hpijx to understand why (it is linked to memory size questions) */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   }       survival function given by stepm (the optimization length). Unfortunately it
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);       means that if the survival funtion is printed every two years of age and if
   fprintf(ficrespl,"#Prevalence limit\n");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   fprintf(ficrespl,"#Age ");       results. So we changed our mind and took the option of the best precision.
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    */
   fprintf(ficrespl,"\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      agelim = AGESUP;
   prlim=matrix(1,nlstate,1,nlstate);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      gp=matrix(0,nhstepm,1,nlstate);
   k=0;      gm=matrix(0,nhstepm,1,nlstate);
   agebase=ageminpar;  
   agelim=agemaxpar;  
   ftolpl=1.e-10;      for(theta=1; theta <=npar; theta++){
   i1=cptcoveff;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   if (cptcovn < 1){i1=1;}          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
   for(cptcov=1;cptcov<=i1;cptcov++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        if (popbased==1) {
         fprintf(ficrespl,"\n#******");          if(mobilav ==0){
         for(j=1;j<=cptcoveff;j++)            for(i=1; i<=nlstate;i++)
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              prlim[i][i]=probs[(int)age][i][ij];
         fprintf(ficrespl,"******\n");          }else{ /* mobilav */ 
                    for(i=1; i<=nlstate;i++)
         for (age=agebase; age<=agelim; age++){              prlim[i][i]=mobaverage[(int)age][i][ij];
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          }
           fprintf(ficrespl,"%.0f",age );        }
           for(i=1; i<=nlstate;i++)    
           fprintf(ficrespl," %.5f", prlim[i][i]);        for(j=1; j<= nlstate; j++){
           fprintf(ficrespl,"\n");          for(h=0; h<=nhstepm; h++){
         }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
       }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     }          }
   fclose(ficrespl);        }
         /* This for computing probability of death (h=1 means
   /*------------- h Pij x at various ages ------------*/           computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   printf("Computing pij: result on file '%s' \n", filerespij);        }    
          /* end probability of death */
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   /*if (stepm<=24) stepsize=2;*/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   agelim=AGESUP;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   hstepm=stepsize*YEARM; /* Every year of age */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */   
         if (popbased==1) {
   /* hstepm=1;   aff par mois*/          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
   k=0;              prlim[i][i]=probs[(int)age][i][ij];
   for(cptcov=1;cptcov<=i1;cptcov++){          }else{ /* mobilav */ 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            for(i=1; i<=nlstate;i++)
       k=k+1;              prlim[i][i]=mobaverage[(int)age][i][ij];
         fprintf(ficrespij,"\n#****** ");          }
         for(j=1;j<=cptcoveff;j++)        }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
                  for(h=0; h<=nhstepm; h++){
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          }
         }
           /*      nhstepm=nhstepm*YEARM; aff par mois*/        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           as a weighted average of prlim.
           oldm=oldms;savm=savms;        */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(j=nlstate+1;j<=nlstate+ndeath;j++){
           fprintf(ficrespij,"# Age");          for(i=1,gmp[j]=0.; i<= nlstate; i++)
           for(i=1; i<=nlstate;i++)           gmp[j] += prlim[i][i]*p3mat[i][j][1];
             for(j=1; j<=nlstate+ndeath;j++)        }    
               fprintf(ficrespij," %1d-%1d",i,j);        /* end probability of death */
           fprintf(ficrespij,"\n");  
            for (h=0; h<=nhstepm; h++){        for(j=1; j<= nlstate; j++) /* vareij */
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          for(h=0; h<=nhstepm; h++){
             for(i=1; i<=nlstate;i++)            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
               for(j=1; j<=nlstate+ndeath;j++)          }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
              }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
           fprintf(ficrespij,"\n");  
         }      } /* End theta */
     }  
   }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);      for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
   fclose(ficrespij);          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
   /*---------- Forecasting ------------------*/      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   if((stepm == 1) && (strcmp(model,".")==0)){        for(theta=1; theta <=npar; theta++)
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          trgradgp[j][theta]=gradgp[theta][j];
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    
   }  
   else{      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     erreur=108;      for(i=1;i<=nlstate;i++)
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);        for(j=1;j<=nlstate;j++)
   }          vareij[i][j][(int)age] =0.;
    
       for(h=0;h<=nhstepm;h++){
   /*---------- Health expectancies and variances ------------*/        for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   strcpy(filerest,"t");          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   strcat(filerest,fileres);          for(i=1;i<=nlstate;i++)
   if((ficrest=fopen(filerest,"w"))==NULL) {            for(j=1;j<=nlstate;j++)
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   }        }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      }
     
       /* pptj */
   strcpy(filerese,"e");      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   strcat(filerese,fileres);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   if((ficreseij=fopen(filerese,"w"))==NULL) {      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   }          varppt[j][i]=doldmp[j][i];
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      /* end ppptj */
       /*  x centered again */
  strcpy(fileresv,"v");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   strcat(fileresv,fileres);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {   
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      if (popbased==1) {
   }        if(mobilav ==0){
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          for(i=1; i<=nlstate;i++)
   calagedate=-1;            prlim[i][i]=probs[(int)age][i][ij];
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
   k=0;            prlim[i][i]=mobaverage[(int)age][i][ij];
   for(cptcov=1;cptcov<=i1;cptcov++){        }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }
       k=k+1;               
       fprintf(ficrest,"\n#****** ");      /* This for computing probability of death (h=1 means
       for(j=1;j<=cptcoveff;j++)         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         as a weighted average of prlim.
       fprintf(ficrest,"******\n");      */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
       fprintf(ficreseij,"\n#****** ");        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       for(j=1;j<=cptcoveff;j++)          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      }    
       fprintf(ficreseij,"******\n");      /* end probability of death */
   
       fprintf(ficresvij,"\n#****** ");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=1;j<=cptcoveff;j++)      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       fprintf(ficresvij,"******\n");        for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        }
       oldm=oldms;savm=savms;      } 
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);        fprintf(ficresprobmorprev,"\n");
    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      fprintf(ficresvij,"%.0f ",age );
       oldm=oldms;savm=savms;      for(i=1; i<=nlstate;i++)
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);        for(j=1; j<=nlstate;j++){
              fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
        fprintf(ficresvij,"\n");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      free_matrix(gp,0,nhstepm,1,nlstate);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      free_matrix(gm,0,nhstepm,1,nlstate);
       fprintf(ficrest,"\n");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       epj=vector(1,nlstate+1);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(age=bage; age <=fage ;age++){    } /* End age */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    free_vector(gpp,nlstate+1,nlstate+ndeath);
         if (popbased==1) {    free_vector(gmp,nlstate+1,nlstate+ndeath);
           for(i=1; i<=nlstate;i++)    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
             prlim[i][i]=probs[(int)age][i][k];    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(ficrest," %4.0f",age);    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
             epj[j] += prlim[i][i]*eij[i][j][(int)age];  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    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));
           epj[nlstate+1] +=epj[j];    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);
         for(i=1, vepp=0.;i <=nlstate;i++)    /*  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);
           for(j=1;j <=nlstate;j++)  */
             vepp += vareij[i][j][(int)age];  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    free_vector(xp,1,npar);
         }    free_matrix(doldm,1,nlstate,1,nlstate);
         fprintf(ficrest,"\n");    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);
 free_matrix(mint,1,maxwav,1,n);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    fclose(ficresprobmorprev);
     free_vector(weight,1,n);    fflush(ficgp);
   fclose(ficreseij);    fflush(fichtm); 
   fclose(ficresvij);  }  /* end varevsij */
   fclose(ficrest);  
   fclose(ficpar);  /************ Variance of prevlim ******************/
   free_vector(epj,1,nlstate+1);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
    {
   /*------- Variance limit prevalence------*/      /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   strcpy(fileresvpl,"vpl");  
   strcat(fileresvpl,fileres);    double **dnewm,**doldm;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    int i, j, nhstepm, hstepm;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    double *xp;
     exit(0);    double *gp, *gm;
   }    double **gradg, **trgradg;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    double age,agelim;
     int theta;
   k=0;    
   for(cptcov=1;cptcov<=i1;cptcov++){    pstamp(ficresvpl);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
       k=k+1;    fprintf(ficresvpl,"# Age");
       fprintf(ficresvpl,"\n#****** ");    for(i=1; i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++)        fprintf(ficresvpl," %1d-%1d",i,i);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresvpl,"\n");
       fprintf(ficresvpl,"******\n");  
          xp=vector(1,npar);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    dnewm=matrix(1,nlstate,1,npar);
       oldm=oldms;savm=savms;    doldm=matrix(1,nlstate,1,nlstate);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    
     }    hstepm=1*YEARM; /* Every year of age */
  }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
   fclose(ficresvpl);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   /*---------- End : free ----------------*/      if (stepm >= YEARM) hstepm=1;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
        gradg=matrix(1,npar,1,nlstate);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      gp=vector(1,nlstate);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      gm=vector(1,nlstate);
    
        for(theta=1; theta <=npar; theta++){
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        for(i=1; i<=npar; i++){ /* Computes gradient */
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        }
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
          for(i=1;i<=nlstate;i++)
   free_matrix(matcov,1,npar,1,npar);          gp[i] = prlim[i][i];
   free_vector(delti,1,npar);      
   free_matrix(agev,1,maxwav,1,imx);        for(i=1; i<=npar; i++) /* Computes gradient */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   fprintf(fichtm,"\n</body>");        for(i=1;i<=nlstate;i++)
   fclose(fichtm);          gm[i] = prlim[i][i];
   fclose(ficgp);  
          for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   if(erreur >0)      } /* End theta */
     printf("End of Imach with error or warning %d\n",erreur);  
   else   printf("End of Imach\n");      trgradg =matrix(1,nlstate,1,npar);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
        for(j=1; j<=nlstate;j++)
   /* 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);*/        for(theta=1; theta <=npar; theta++)
   /*printf("Total time was %d uSec.\n", total_usecs);*/          trgradg[j][theta]=gradg[theta][j];
   /*------ End -----------*/  
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
  end:      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
 #ifdef windows      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   /* chdir(pathcd);*/      for(i=1;i<=nlstate;i++)
 #endif        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/      fprintf(ficresvpl,"%.0f ",age );
  /*system("cd ../gp37mgw");*/      for(i=1; i<=nlstate;i++)
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
  strcpy(plotcmd,GNUPLOTPROGRAM);      fprintf(ficresvpl,"\n");
  strcat(plotcmd," ");      free_vector(gp,1,nlstate);
  strcat(plotcmd,optionfilegnuplot);      free_vector(gm,1,nlstate);
  system(plotcmd);      free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
 #ifdef windows    } /* End age */
   while (z[0] != 'q') {  
     /* chdir(path); */    free_vector(xp,1,npar);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    free_matrix(doldm,1,nlstate,1,npar);
     scanf("%s",z);    free_matrix(dnewm,1,nlstate,1,nlstate);
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') system(optionfilehtm);  }
     else if (z[0] == 'g') system(plotcmd);  
     else if (z[0] == 'q') exit(0);  /************ 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[])
 #endif  {
 }    int i, j=0,  k1, l1, tj;
     int k2, l2, j1,  z1;
     int k=0, l;
     int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age, cov[NCOVMAX+1];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     /* tj=cptcoveff; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));
         gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } */ /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   void 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*************/
   void 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);
   }
   
   int 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 = *nberr + 1;
           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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           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;
                 }
               }
             } /* agedc > 0 */
           }
           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);
   }
   
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
      /* #include <gnu/libc-version.h> */ /* Only on gnu */
   
      printf("Compiled with:");fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(". ");fprintf(ficlog,". ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
   #elif __unix__ // all unices, not all compilers
       // Unix
   #elif __linux__
       // linux
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though...
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   #include <stdint.h>
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit."); /* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
     printf(" 64-bit.");/* 64-bit */
   #else
    printf(" wtf-bit."); /* wtf */
   #endif
   
   struct utsname sysInfo;
   
      if (uname(&sysInfo) != -1) {
        printf(" %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog," %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf("GNU C version %d.\n", __GNUC_VERSION__);
      fprintf(ficlog, "GNU C version %d.\n", __GNUC_VERSION__);
   #endif
   #if defined(_MSC_VER)
      printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);
      fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);
   #endif
      
     /* printf("GNU libc version: %s\n", gnu_get_libc_version()); */
   
    }
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Directory already exists (or can't create it) %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);
   
     syscompilerinfo();
   
     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.1.49  
changed lines
  Added in v.1.169


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