Diff for /imach/src/imach.c between versions 1.50 and 1.173

version 1.50, 2002/06/26 23:25:02 version 1.173, 2015/01/03 12:06:26
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.173  2015/01/03 12:06:26  brouard
      Summary: trying to detect cross-compilation
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.172  2014/12/27 12:07:47  brouard
   first survey ("cross") where individuals from different ages are    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.171  2014/12/23 13:26:59  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: Back from Visual C
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Still problem with utsname.h on Windows
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.170  2014/12/23 11:17:12  brouard
   simplest model is the multinomial logistic model where pij is the    Summary: Cleaning some \%% back to %%
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    The escape was mandatory for a specific compiler (which one?), but too many warnings.
   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 1.169  2014/12/22 23:08:31  brouard
   complex model than "constant and age", you should modify the program    Summary: 0.98p
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Outputs some informations on compiler used, OS etc. Testing on different platforms.
   convergence.  
     Revision 1.168  2014/12/22 15:17:42  brouard
   The advantage of this computer programme, compared to a simple    Summary: update
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.167  2014/12/22 13:50:56  brouard
   intermediate interview, the information is lost, but taken into    Summary: Testing uname and compiler version and if compiled 32 or 64
   account using an interpolation or extrapolation.    
     Testing on Linux 64
   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 1.166  2014/12/22 11:40:47  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    *** empty log message ***
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.165  2014/12/16 11:20:36  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    Summary: After compiling on Visual C
   and the contribution of each individual to the likelihood is simply  
   hPijx.    * imach.c (Module): Merging 1.61 to 1.162
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.164  2014/12/16 10:52:11  brouard
   of the life expectancies. It also computes the prevalence limits.    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    * imach.c (Module): Merging 1.61 to 1.162
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.163  2014/12/16 10:30:11  brouard
   from the European Union.    * imach.c (Module): Merging 1.61 to 1.162
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.162  2014/09/25 11:43:39  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Summary: temporary backup 0.99!
   **********************************************************************/  
      Revision 1.1  2014/09/16 11:06:58  brouard
 #include <math.h>    Summary: With some code (wrong) for nlopt
 #include <stdio.h>  
 #include <stdlib.h>    Author:
 #include <unistd.h>  
     Revision 1.161  2014/09/15 20:41:41  brouard
 #define MAXLINE 256    Summary: Problem with macro SQR on Intel compiler
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.160  2014/09/02 09:24:05  brouard
 #define FILENAMELENGTH 80    *** empty log message ***
 /*#define DEBUG*/  
 #define windows    Revision 1.159  2014/09/01 10:34:10  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Summary: WIN32
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Author: Brouard
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.158  2014/08/27 17:11:51  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    *** empty log message ***
   
 #define NINTERVMAX 8    Revision 1.157  2014/08/27 16:26:55  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Summary: Preparing windows Visual studio version
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Author: Brouard
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    In order to compile on Visual studio, time.h is now correct and time_t
 #define YEARM 12. /* Number of months per year */    and tm struct should be used. difftime should be used but sometimes I
 #define AGESUP 130    just make the differences in raw time format (time(&now).
 #define AGEBASE 40    Trying to suppress #ifdef LINUX
 #ifdef windows    Add xdg-open for __linux in order to open default browser.
 #define DIRSEPARATOR '\\'  
 #define ODIRSEPARATOR '/'    Revision 1.156  2014/08/25 20:10:10  brouard
 #else    *** empty log message ***
 #define DIRSEPARATOR '/'  
 #define ODIRSEPARATOR '\\'    Revision 1.155  2014/08/25 18:32:34  brouard
 #endif    Summary: New compile, minor changes
     Author: Brouard
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";  
 int erreur; /* Error number */    Revision 1.154  2014/06/20 17:32:08  brouard
 int nvar;    Summary: Outputs now all graphs of convergence to period prevalence
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.153  2014/06/20 16:45:46  brouard
 int nlstate=2; /* Number of live states */    Summary: If 3 live state, convergence to period prevalence on same graph
 int ndeath=1; /* Number of dead states */    Author: Brouard
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.152  2014/06/18 17:54:09  brouard
     Summary: open browser, use gnuplot on same dir than imach if not found in the path
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.151  2014/06/18 16:43:30  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    *** empty log message ***
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.150  2014/06/18 16:42:35  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 double jmean; /* Mean space between 2 waves */    Author: brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.149  2014/06/18 15:51:14  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Summary: Some fixes in parameter files errors
 FILE *ficlog;    Author: Nicolas Brouard
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *ficresprobmorprev;    Revision 1.148  2014/06/17 17:38:48  brouard
 FILE *fichtm; /* Html File */    Summary: Nothing new
 FILE *ficreseij;    Author: Brouard
 char filerese[FILENAMELENGTH];  
 FILE  *ficresvij;    Just a new packaging for OS/X version 0.98nS
 char fileresv[FILENAMELENGTH];  
 FILE  *ficresvpl;    Revision 1.147  2014/06/16 10:33:11  brouard
 char fileresvpl[FILENAMELENGTH];    *** empty log message ***
 char title[MAXLINE];  
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    Revision 1.146  2014/06/16 10:20:28  brouard
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    Summary: Merge
     Author: Brouard
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
 char filelog[FILENAMELENGTH]; /* Log file */    Merge, before building revised version.
 char filerest[FILENAMELENGTH];  
 char fileregp[FILENAMELENGTH];    Revision 1.145  2014/06/10 21:23:15  brouard
 char popfile[FILENAMELENGTH];    Summary: Debugging with valgrind
     Author: Nicolas Brouard
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  
     Lot of changes in order to output the results with some covariates
 #define NR_END 1    After the Edimburgh REVES conference 2014, it seems mandatory to
 #define FREE_ARG char*    improve the code.
 #define FTOL 1.0e-10    No more memory valgrind error but a lot has to be done in order to
     continue the work of splitting the code into subroutines.
 #define NRANSI    Also, decodemodel has been improved. Tricode is still not
 #define ITMAX 200    optimal. nbcode should be improved. Documentation has been added in
     the source code.
 #define TOL 2.0e-4  
     Revision 1.143  2014/01/26 09:45:38  brouard
 #define CGOLD 0.3819660    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
     (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.142  2014/01/26 03:57:36  brouard
 #define TINY 1.0e-20    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   
 static double maxarg1,maxarg2;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    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 SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.140  2011/09/02 10:37:54  brouard
     Summary: times.h is ok with mingw32 now.
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.139  2010/06/14 07:50:17  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
     I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 int imx;  
 int stepm;    Revision 1.138  2010/04/30 18:19:40  brouard
 /* Stepm, step in month: minimum step interpolation*/    *** empty log message ***
   
 int estepm;    Revision 1.137  2010/04/29 18:11:38  brouard
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    (Module): Checking covariates for more complex models
     than V1+V2. A lot of change to be done. Unstable.
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.136  2010/04/26 20:30:53  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (Module): merging some libgsl code. Fixing computation
 double **pmmij, ***probs, ***mobaverage;    of likelione (using inter/intrapolation if mle = 0) in order to
 double dateintmean=0;    get same likelihood as if mle=1.
     Some cleaning of code and comments added.
 double *weight;  
 int **s; /* Status */    Revision 1.135  2009/10/29 15:33:14  brouard
 double *agedc, **covar, idx;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.134  2009/10/29 13:18:53  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.133  2009/07/06 10:21:25  brouard
 /**************** split *************************/    just nforces
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.132  2009/07/06 08:22:05  brouard
    char *s;                             /* pointer */    Many tings
    int  l1, l2;                         /* length counters */  
     Revision 1.131  2009/06/20 16:22:47  brouard
    l1 = strlen( path );                 /* length of path */    Some dimensions resccaled
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    Revision 1.130  2009/05/26 06:44:34  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    (Module): Max Covariate is now set to 20 instead of 8. A
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)    lot of cleaning with variables initialized to 0. Trying to make
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    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
       if ( getwd( dirc ) == NULL ) {  
 #else    Revision 1.128  2006/06/30 13:02:05  brouard
       extern char       *getcwd( );    (Module): Clarifications on computing e.j
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.127  2006/04/28 18:11:50  brouard
 #endif    (Module): Yes the sum of survivors was wrong since
          return( GLOCK_ERROR_GETCWD );    imach-114 because nhstepm was no more computed in the age
       }    loop. Now we define nhstepma in the age loop.
       strcpy( name, path );             /* we've got it */    (Module): In order to speed up (in case of numerous covariates) we
    } else {                             /* strip direcotry from path */    compute health expectancies (without variances) in a first step
       s++;                              /* after this, the filename */    and then all the health expectancies with variances or standard
       l2 = strlen( s );                 /* length of filename */    deviation (needs data from the Hessian matrices) which slows the
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    computation.
       strcpy( name, s );                /* save file name */    In the future we should be able to stop the program is only health
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    expectancies and graph are needed without standard deviations.
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.126  2006/04/28 17:23:28  brouard
    l1 = strlen( dirc );                 /* length of directory */    (Module): Yes the sum of survivors was wrong since
 #ifdef windows    imach-114 because nhstepm was no more computed in the age
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    loop. Now we define nhstepma in the age loop.
 #else    Version 0.98h
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.125  2006/04/04 15:20:31  lievre
    s = strrchr( name, '.' );            /* find last / */    Errors in calculation of health expectancies. Age was not initialized.
    s++;    Forecasting file added.
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Revision 1.124  2006/03/22 17:13:53  lievre
    l2= strlen( s)+1;    Parameters are printed with %lf instead of %f (more numbers after the comma).
    strncpy( finame, name, l1-l2);    The log-likelihood is printed in the log file
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    Revision 1.123  2006/03/20 10:52:43  brouard
 }    * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
   
 /******************************************/    * imach.c (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 void replace(char *s, char*t)    otherwise the weight is truncated).
 {    Modification of warning when the covariates values are not 0 or
   int i;    1.
   int lg=20;    Version 0.98g
   i=0;  
   lg=strlen(t);    Revision 1.122  2006/03/20 09:45:41  brouard
   for(i=0; i<= lg; i++) {    (Module): Weights can have a decimal point as for
     (s[i] = t[i]);    English (a comma might work with a correct LC_NUMERIC environment,
     if (t[i]== '\\') s[i]='/';    otherwise the weight is truncated).
   }    Modification of warning when the covariates values are not 0 or
 }    1.
     Version 0.98g
 int nbocc(char *s, char occ)  
 {    Revision 1.121  2006/03/16 17:45:01  lievre
   int i,j=0;    * imach.c (Module): Comments concerning covariates added
   int lg=20;  
   i=0;    * imach.c (Module): refinements in the computation of lli if
   lg=strlen(s);    status=-2 in order to have more reliable computation if stepm is
   for(i=0; i<= lg; i++) {    not 1 month. Version 0.98f
   if  (s[i] == occ ) j++;  
   }    Revision 1.120  2006/03/16 15:10:38  lievre
   return j;    (Module): refinements in the computation of lli if
 }    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.119  2006/03/15 17:42:26  brouard
   /* cuts string t into u and v where u is ended by char occ excluding it    (Module): Bug if status = -2, the loglikelihood was
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    computed as likelihood omitting the logarithm. Version O.98e
      gives u="abcedf" and v="ghi2j" */  
   int i,lg,j,p=0;    Revision 1.118  2006/03/14 18:20:07  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 1.117  2006/03/14 17:16:22  brouard
     (u[j] = t[j]);    (Module): varevsij Comments added explaining the second
   }    table of variances if popbased=1 .
      u[p]='\0';    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
    for(j=0; j<= lg; j++) {    (Module): Version 0.98d
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.116  2006/03/06 10:29:27  brouard
 }    (Module): Variance-covariance wrong links and
     varian-covariance of ej. is needed (Saito).
 /********************** nrerror ********************/  
     Revision 1.115  2006/02/27 12:17:45  brouard
 void nrerror(char error_text[])    (Module): One freematrix added in mlikeli! 0.98c
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.114  2006/02/26 12:57:58  brouard
   fprintf(stderr,"%s\n",error_text);    (Module): Some improvements in processing parameter
   exit(1);    filename with strsep.
 }  
 /*********************** vector *******************/    Revision 1.113  2006/02/24 14:20:24  brouard
 double *vector(int nl, int nh)    (Module): Memory leaks checks with valgrind and:
 {    datafile was not closed, some imatrix were not freed and on matrix
   double *v;    allocation too.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    Revision 1.112  2006/01/30 09:55:26  brouard
   return v-nl+NR_END;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 }  
     Revision 1.111  2006/01/25 20:38:18  brouard
 /************************ free vector ******************/    (Module): Lots of cleaning and bugs added (Gompertz)
 void free_vector(double*v, int nl, int nh)    (Module): Comments can be added in data file. Missing date values
 {    can be a simple dot '.'.
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Revision 1.109  2006/01/24 19:37:15  brouard
 {    (Module): Comments (lines starting with a #) are allowed in data.
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Revision 1.108  2006/01/19 18:05:42  lievre
   if (!v) nrerror("allocation failure in ivector");    Gnuplot problem appeared...
   return v-nl+NR_END;    To be fixed
 }  
     Revision 1.107  2006/01/19 16:20:37  brouard
 /******************free ivector **************************/    Test existence of gnuplot in imach path
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.106  2006/01/19 13:24:36  brouard
   free((FREE_ARG)(v+nl-NR_END));    Some cleaning and links added in html output
 }  
     Revision 1.105  2006/01/05 20:23:19  lievre
 /******************* imatrix *******************************/    *** empty log message ***
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Revision 1.104  2005/09/30 16:11:43  lievre
 {    (Module): sump fixed, loop imx fixed, and simplifications.
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    (Module): If the status is missing at the last wave but we know
   int **m;    that the person is alive, then we can code his/her status as -2
      (instead of missing=-1 in earlier versions) and his/her
   /* allocate pointers to rows */    contributions to the likelihood is 1 - Prob of dying from last
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   if (!m) nrerror("allocation failure 1 in matrix()");    the healthy state at last known wave). Version is 0.98
   m += NR_END;  
   m -= nrl;    Revision 1.103  2005/09/30 15:54:49  lievre
      (Module): sump fixed, loop imx fixed, and simplifications.
    
   /* allocate rows and set pointers to them */    Revision 1.102  2004/09/15 17:31:30  brouard
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Add the possibility to read data file including tab characters.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.101  2004/09/15 10:38:38  brouard
   m[nrl] -= ncl;    Fix on curr_time
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    Revision 1.100  2004/07/12 18:29:06  brouard
      Add version for Mac OS X. Just define UNIX in Makefile
   /* return pointer to array of pointers to rows */  
   return m;    Revision 1.99  2004/06/05 08:57:40  brouard
 }    *** empty log message ***
   
 /****************** free_imatrix *************************/    Revision 1.98  2004/05/16 15:05:56  brouard
 void free_imatrix(m,nrl,nrh,ncl,nch)    New version 0.97 . First attempt to estimate force of mortality
       int **m;    directly from the data i.e. without the need of knowing the health
       long nch,ncl,nrh,nrl;    state at each age, but using a Gompertz model: log u =a + b*age .
      /* free an int matrix allocated by imatrix() */    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
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    cross-longitudinal survey is different from the mortality estimated
   free((FREE_ARG) (m+nrl-NR_END));    from other sources like vital statistic data.
 }  
     The same imach parameter file can be used but the option for mle should be -3.
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    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.
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    The output is very simple: only an estimate of the intercept and of
     the slope with 95% confident intervals.
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Current limitations:
   m += NR_END;    A) Even if you enter covariates, i.e. with the
   m -= nrl;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     B) There is no computation of Life Expectancy nor Life Table.
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.97  2004/02/20 13:25:42  lievre
   m[nrl] += NR_END;    Version 0.96d. Population forecasting command line is (temporarily)
   m[nrl] -= ncl;    suppressed.
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.96  2003/07/15 15:38:55  brouard
   return m;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 }    rewritten within the same printf. Workaround: many printfs.
   
 /*************************free matrix ************************/    Revision 1.95  2003/07/08 07:54:34  brouard
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    * imach.c (Repository):
 {    (Repository): Using imachwizard code to output a more meaningful covariance
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    matrix (cov(a12,c31) instead of numbers.
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Revision 1.93  2003/06/25 16:33:55  brouard
 {    (Module): On windows (cygwin) function asctime_r doesn't
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    exist so I changed back to asctime which exists.
   double ***m;    (Module): Version 0.96b
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Revision 1.92  2003/06/25 16:30:45  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): On windows (cygwin) function asctime_r doesn't
   m += NR_END;    exist so I changed back to asctime which exists.
   m -= nrl;  
     Revision 1.91  2003/06/25 15:30:29  brouard
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    * imach.c (Repository): Duplicated warning errors corrected.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    (Repository): Elapsed time after each iteration is now output. It
   m[nrl] += NR_END;    helps to forecast when convergence will be reached. Elapsed time
   m[nrl] -= ncl;    is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
     Revision 1.90  2003/06/24 12:34:15  brouard
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    (Module): Some bugs corrected for windows. Also, when
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    mle=-1 a template is output in file "or"mypar.txt with the design
   m[nrl][ncl] += NR_END;    of the covariance matrix to be input.
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)    Revision 1.89  2003/06/24 12:30:52  brouard
     m[nrl][j]=m[nrl][j-1]+nlay;    (Module): Some bugs corrected for windows. Also, when
      mle=-1 a template is output in file "or"mypar.txt with the design
   for (i=nrl+1; i<=nrh; i++) {    of the covariance matrix to be input.
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    Revision 1.88  2003/06/23 17:54:56  brouard
       m[i][j]=m[i][j-1]+nlay;    * 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.
   }  
   return m;    Revision 1.87  2003/06/18 12:26:01  brouard
 }    Version 0.96
   
 /*************************free ma3x ************************/    Revision 1.86  2003/06/17 20:04:08  brouard
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    (Module): Change position of html and gnuplot routines and added
 {    routine fileappend.
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Revision 1.85  2003/06/17 13:12:43  brouard
   free((FREE_ARG)(m+nrl-NR_END));    * imach.c (Repository): Check when date of death was earlier that
 }    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 /***************** f1dim *************************/    was wrong (infinity). We still send an "Error" but patch by
 extern int ncom;    assuming that the date of death was just one stepm after the
 extern double *pcom,*xicom;    interview.
 extern double (*nrfunc)(double []);    (Repository): Because some people have very long ID (first column)
      we changed int to long in num[] and we added a new lvector for
 double f1dim(double x)    memory allocation. But we also truncated to 8 characters (left
 {    truncation)
   int j;    (Repository): No more line truncation errors.
   double f;  
   double *xt;    Revision 1.84  2003/06/13 21:44:43  brouard
      * imach.c (Repository): Replace "freqsummary" at a correct
   xt=vector(1,ncom);    place. It differs from routine "prevalence" which may be called
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    many times. Probs is memory consuming and must be used with
   f=(*nrfunc)(xt);    parcimony.
   free_vector(xt,1,ncom);    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   return f;  
 }    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    Revision 1.82  2003/06/05 15:57:20  brouard
 {    Add log in  imach.c and  fullversion number is now printed.
   int iter;  
   double a,b,d,etemp;  */
   double fu,fv,fw,fx;  /*
   double ftemp;     Interpolated Markov Chain
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;    Short summary of the programme:
      
   a=(ax < cx ? ax : cx);    This program computes Healthy Life Expectancies from
   b=(ax > cx ? ax : cx);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   x=w=v=bx;    first survey ("cross") where individuals from different ages are
   fw=fv=fx=(*f)(x);    interviewed on their health status or degree of disability (in the
   for (iter=1;iter<=ITMAX;iter++) {    case of a health survey which is our main interest) -2- at least a
     xm=0.5*(a+b);    second wave of interviews ("longitudinal") which measure each change
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    (if any) in individual health status.  Health expectancies are
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    computed from the time spent in each health state according to a
     printf(".");fflush(stdout);    model. More health states you consider, more time is necessary to reach the
     fprintf(ficlog,".");fflush(ficlog);    Maximum Likelihood of the parameters involved in the model.  The
 #ifdef DEBUG    simplest model is the multinomial logistic model where pij is the
     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);    probability to be observed in state j at the second wave
     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);    conditional to be observed in state i at the first wave. Therefore
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #endif    'age' is age and 'sex' is a covariate. If you want to have a more
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    complex model than "constant and age", you should modify the program
       *xmin=x;    where the markup *Covariates have to be included here again* invites
       return fx;    you to do it.  More covariates you add, slower the
     }    convergence.
     ftemp=fu;  
     if (fabs(e) > tol1) {    The advantage of this computer programme, compared to a simple
       r=(x-w)*(fx-fv);    multinomial logistic model, is clear when the delay between waves is not
       q=(x-v)*(fx-fw);    identical for each individual. Also, if a individual missed an
       p=(x-v)*q-(x-w)*r;    intermediate interview, the information is lost, but taken into
       q=2.0*(q-r);    account using an interpolation or extrapolation.  
       if (q > 0.0) p = -p;  
       q=fabs(q);    hPijx is the probability to be observed in state i at age x+h
       etemp=e;    conditional to the observed state i at age x. The delay 'h' can be
       e=d;    split into an exact number (nh*stepm) of unobserved intermediate
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    states. This elementary transition (by month, quarter,
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    semester or year) is modelled as a multinomial logistic.  The hPx
       else {    matrix is simply the matrix product of nh*stepm elementary matrices
         d=p/q;    and the contribution of each individual to the likelihood is simply
         u=x+d;    hPijx.
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);    Also this programme outputs the covariance matrix of the parameters but also
       }    of the life expectancies. It also computes the period (stable) prevalence. 
     } else {    
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
     }             Institut national d'études démographiques, Paris.
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    This software have been partly granted by Euro-REVES, a concerted action
     fu=(*f)(u);    from the European Union.
     if (fu <= fx) {    It is copyrighted identically to a GNU software product, ie programme and
       if (u >= x) a=x; else b=x;    software can be distributed freely for non commercial use. Latest version
       SHFT(v,w,x,u)    can be accessed at http://euroreves.ined.fr/imach .
         SHFT(fv,fw,fx,fu)  
         } else {    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
           if (u < x) a=u; else b=u;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
           if (fu <= fw || w == x) {    
             v=w;    **********************************************************************/
             w=u;  /*
             fv=fw;    main
             fw=fu;    read parameterfile
           } else if (fu <= fv || v == x || v == w) {    read datafile
             v=u;    concatwav
             fv=fu;    freqsummary
           }    if (mle >= 1)
         }      mlikeli
   }    print results files
   nrerror("Too many iterations in brent");    if mle==1 
   *xmin=x;       computes hessian
   return fx;    read end of parameter file: agemin, agemax, bage, fage, estepm
 }        begin-prev-date,...
     open gnuplot file
 /****************** mnbrak ***********************/    open html file
     period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
             double (*func)(double))                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
 {      freexexit2 possible for memory heap.
   double ulim,u,r,q, dum;  
   double fu;    h Pij x                         | pij_nom  ficrestpij
       # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   *fa=(*func)(*ax);         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
   *fb=(*func)(*bx);         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
       SHFT(dum,*fb,*fa,dum)         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
       }    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   *cx=(*bx)+GOLD*(*bx-*ax);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   *fc=(*func)(*cx);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);    forecasting if prevfcast==1 prevforecast call prevalence()
     q=(*bx-*cx)*(*fb-*fa);    health expectancies
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    Variance-covariance of DFLE
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    prevalence()
     ulim=(*bx)+GLIMIT*(*cx-*bx);     movingaverage()
     if ((*bx-u)*(u-*cx) > 0.0) {    varevsij() 
       fu=(*func)(u);    if popbased==1 varevsij(,popbased)
     } else if ((*cx-u)*(u-ulim) > 0.0) {    total life expectancies
       fu=(*func)(u);    Variance of period (stable) prevalence
       if (fu < *fc) {   end
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  */
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  #define POWELL /* Instead of NLOPT */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  #include <math.h>
       fu=(*func)(u);  #include <stdio.h>
     } else {  #include <stdlib.h>
       u=(*cx)+GOLD*(*cx-*bx);  #include <string.h>
       fu=(*func)(u);  
     }  #ifdef _WIN32
     SHFT(*ax,*bx,*cx,u)  #include <io.h>
       SHFT(*fa,*fb,*fc,fu)  #include <windows.h>
       }  #include <tchar.h>
 }  #else
   #include <unistd.h>
 /*************** linmin ************************/  #endif
   
 int ncom;  #include <limits.h>
 double *pcom,*xicom;  #include <sys/types.h>
 double (*nrfunc)(double []);  
    #if defined(__GNUC__)
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  #include <sys/utsname.h> /* Doesn't work on Windows */
 {  #endif
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);  #include <sys/stat.h>
   double f1dim(double x);  #include <errno.h>
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /* extern int errno; */
               double *fc, double (*func)(double));  
   int j;  /* #ifdef LINUX */
   double xx,xmin,bx,ax;  /* #include <time.h> */
   double fx,fb,fa;  /* #include "timeval.h" */
    /* #else */
   ncom=n;  /* #include <sys/time.h> */
   pcom=vector(1,n);  /* #endif */
   xicom=vector(1,n);  
   nrfunc=func;  #include <time.h>
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  #ifdef GSL
     xicom[j]=xi[j];  #include <gsl/gsl_errno.h>
   }  #include <gsl/gsl_multimin.h>
   ax=0.0;  #endif
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #ifdef NLOPT
 #ifdef DEBUG  #include <nlopt.h>
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  typedef struct {
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    double (* function)(double [] );
 #endif  } myfunc_data ;
   for (j=1;j<=n;j++) {  #endif
     xi[j] *= xmin;  
     p[j] += xi[j];  /* #include <libintl.h> */
   }  /* #define _(String) gettext (String) */
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
 }  
   #define GNUPLOTPROGRAM "gnuplot"
 /*************** powell ************************/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #define FILENAMELENGTH 132
             double (*func)(double []))  
 {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   void linmin(double p[], double xi[], int n, double *fret,  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
               double (*func)(double []));  
   int i,ibig,j;  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
   double del,t,*pt,*ptt,*xit;  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
   double fp,fptt;  
   double *xits;  #define NINTERVMAX 8
   pt=vector(1,n);  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
   ptt=vector(1,n);  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
   xit=vector(1,n);  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
   xits=vector(1,n);  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
   *fret=(*func)(p);  #define MAXN 20000
   for (j=1;j<=n;j++) pt[j]=p[j];  #define YEARM 12. /**< Number of months per year */
   for (*iter=1;;++(*iter)) {  #define AGESUP 130
     fp=(*fret);  #define AGEBASE 40
     ibig=0;  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
     del=0.0;  #ifdef _WIN32
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #define DIRSEPARATOR '\\'
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #define CHARSEPARATOR "\\"
     for (i=1;i<=n;i++)  #define ODIRSEPARATOR '/'
       printf(" %d %.12f",i, p[i]);  #else
     fprintf(ficlog," %d %.12f",i, p[i]);  #define DIRSEPARATOR '/'
     printf("\n");  #define CHARSEPARATOR "/"
     fprintf(ficlog,"\n");  #define ODIRSEPARATOR '\\'
     for (i=1;i<=n;i++) {  #endif
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  /* $Id$ */
 #ifdef DEBUG  /* $State$ */
       printf("fret=%lf \n",*fret);  
       fprintf(ficlog,"fret=%lf \n",*fret);  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";
 #endif  char fullversion[]="$Revision$ $Date$"; 
       printf("%d",i);fflush(stdout);  char strstart[80];
       fprintf(ficlog,"%d",i);fflush(ficlog);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       linmin(p,xit,n,fret,func);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
       if (fabs(fptt-(*fret)) > del) {  int nvar=0, nforce=0; /* Number of variables, number of forces */
         del=fabs(fptt-(*fret));  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
         ibig=i;  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
       }  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
 #ifdef DEBUG  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
       printf("%d %.12e",i,(*fret));  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
       fprintf(ficlog,"%d %.12e",i,(*fret));  int cptcovprodnoage=0; /**< Number of covariate products without age */   
       for (j=1;j<=n;j++) {  int cptcoveff=0; /* Total number of covariates to vary for printing results */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  int cptcov=0; /* Working variable */
         printf(" x(%d)=%.12e",j,xit[j]);  int npar=NPARMAX;
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  int nlstate=2; /* Number of live states */
       }  int ndeath=1; /* Number of dead states */
       for(j=1;j<=n;j++) {  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
         printf(" p=%.12e",p[j]);  int popbased=0;
         fprintf(ficlog," p=%.12e",p[j]);  
       }  int *wav; /* Number of waves for this individuual 0 is possible */
       printf("\n");  int maxwav=0; /* Maxim number of waves */
       fprintf(ficlog,"\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. */
       fprintf(ficlog,"Max: %.12e",(*func)(p));  int countcallfunc=0;  /* Count the number of calls to func */
       for (j=1;j<=n;j++) {  double jmean=1; /* Mean space between 2 waves */
         printf(" %.12e",p[j]);  double **matprod2(); /* test */
         fprintf(ficlog," %.12e",p[j]);  double **oldm, **newm, **savm; /* Working pointers to matrices */
       }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       printf("\n");  /*FILE *fic ; */ /* Used in readdata only */
       fprintf(ficlog,"\n");  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       for(l=0;l<=1;l++) {  FILE *ficlog, *ficrespow;
         for (j=1;j<=n;j++) {  int globpr=0; /* Global variable for printing or not */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  double fretone; /* Only one call to likelihood */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  long ipmx=0; /* Number of contributions */
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  double sw; /* Sum of weights */
         }  char filerespow[FILENAMELENGTH];
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  FILE *ficresilk;
       }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #endif  FILE *ficresprobmorprev;
   FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
       free_vector(xit,1,n);  char filerese[FILENAMELENGTH];
       free_vector(xits,1,n);  FILE *ficresstdeij;
       free_vector(ptt,1,n);  char fileresstde[FILENAMELENGTH];
       free_vector(pt,1,n);  FILE *ficrescveij;
       return;  char filerescve[FILENAMELENGTH];
     }  FILE  *ficresvij;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  char fileresv[FILENAMELENGTH];
     for (j=1;j<=n;j++) {  FILE  *ficresvpl;
       ptt[j]=2.0*p[j]-pt[j];  char fileresvpl[FILENAMELENGTH];
       xit[j]=p[j]-pt[j];  char title[MAXLINE];
       pt[j]=p[j];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     }  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     fptt=(*func)(ptt);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     if (fptt < fp) {  char command[FILENAMELENGTH];
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  int  outcmd=0;
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         for (j=1;j<=n;j++) {  
           xi[j][ibig]=xi[j][n];  char filelog[FILENAMELENGTH]; /* Log file */
           xi[j][n]=xit[j];  char filerest[FILENAMELENGTH];
         }  char fileregp[FILENAMELENGTH];
 #ifdef DEBUG  char popfile[FILENAMELENGTH];
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
         for(j=1;j<=n;j++){  
           printf(" %.12e",xit[j]);  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
           fprintf(ficlog," %.12e",xit[j]);  /* struct timezone tzp; */
         }  /* extern int gettimeofday(); */
         printf("\n");  struct tm tml, *gmtime(), *localtime();
         fprintf(ficlog,"\n");  
 #endif  extern time_t time();
       }  
     }  struct tm start_time, end_time, curr_time, last_time, forecast_time;
   }  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
 }  struct tm tm;
   
 /**** Prevalence limit ****************/  char strcurr[80], strfor[80];
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  char *endptr;
 {  long lval;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  double dval;
      matrix by transitions matrix until convergence is reached */  
   #define NR_END 1
   int i, ii,j,k;  #define FREE_ARG char*
   double min, max, maxmin, maxmax,sumnew=0.;  #define FTOL 1.0e-10
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  #define NRANSI 
   double **newm;  #define ITMAX 200 
   double agefin, delaymax=50 ; /* Max number of years to converge */  
   #define TOL 2.0e-4 
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  #define CGOLD 0.3819660 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  #define ZEPS 1.0e-10 
     }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
    cov[1]=1.;  #define GOLD 1.618034 
    #define GLIMIT 100.0 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  #define TINY 1.0e-20 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;  static double maxarg1,maxarg2;
     /* Covariates have to be included here again */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
      cov[2]=agefin;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
      
       for (k=1; k<=cptcovn;k++) {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #define rint(a) floor(a+0.5)
         /*      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]]);*/  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
       }  /* #define mytinydouble 1.0e-16 */
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
       for (k=1; k<=cptcovprod;k++)  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /* static double dsqrarg; */
   /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  static double sqrarg;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  int agegomp= AGEGOMP;
   
     savm=oldm;  int imx; 
     oldm=newm;  int stepm=1;
     maxmax=0.;  /* Stepm, step in month: minimum step interpolation*/
     for(j=1;j<=nlstate;j++){  
       min=1.;  int estepm;
       max=0.;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  int m,nb;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  long *num;
         prlim[i][j]= newm[i][j]/(1-sumnew);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
         max=FMAX(max,prlim[i][j]);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
         min=FMIN(min,prlim[i][j]);  double **pmmij, ***probs;
       }  double *ageexmed,*agecens;
       maxmin=max-min;  double dateintmean=0;
       maxmax=FMAX(maxmax,maxmin);  
     }  double *weight;
     if(maxmax < ftolpl){  int **s; /* Status */
       return prlim;  double *agedc;
     }  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
   }                    * covar=matrix(0,NCOVMAX,1,n); 
 }                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
   double  idx; 
 /*************** transition probabilities ***************/  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   int *Ndum; /** Freq of modality (tricode */
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  int **codtab; /**< codtab=imatrix(1,100,1,10); */
 {  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
   double s1, s2;  double *lsurv, *lpop, *tpop;
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   double ftolhess; /**< Tolerance for computing hessian */
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){  /**************** split *************************/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
         /*s2 += param[i][j][nc]*cov[nc];*/  {
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       }    */ 
       ps[i][j]=s2;    char  *ss;                            /* pointer */
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    int   l1, l2;                         /* length counters */
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){    l1 = strlen(path );                   /* length of path */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       }      strcpy( name, path );               /* we got the fullname name because no directory */
       ps[i][j]=s2;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     }        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   }      /* get current working directory */
     /*ps[3][2]=1;*/      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   for(i=1; i<= nlstate; i++){        return( GLOCK_ERROR_GETCWD );
      s1=0;      }
     for(j=1; j<i; j++)      /* got dirc from getcwd*/
       s1+=exp(ps[i][j]);      printf(" DIRC = %s \n",dirc);
     for(j=i+1; j<=nlstate+ndeath; j++)    } else {                              /* strip direcotry from path */
       s1+=exp(ps[i][j]);      ss++;                               /* after this, the filename */
     ps[i][i]=1./(s1+1.);      l2 = strlen( ss );                  /* length of filename */
     for(j=1; j<i; j++)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       ps[i][j]= exp(ps[i][j])*ps[i][i];      strcpy( name, ss );         /* save file name */
     for(j=i+1; j<=nlstate+ndeath; j++)      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       ps[i][j]= exp(ps[i][j])*ps[i][i];      dirc[l1-l2] = 0;                    /* add zero */
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      printf(" DIRC2 = %s \n",dirc);
   } /* end i */    }
     /* We add a separator at the end of dirc if not exists */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    l1 = strlen( dirc );                  /* length of directory */
     for(jj=1; jj<= nlstate+ndeath; jj++){    if( dirc[l1-1] != DIRSEPARATOR ){
       ps[ii][jj]=0;      dirc[l1] =  DIRSEPARATOR;
       ps[ii][ii]=1;      dirc[l1+1] = 0; 
     }      printf(" DIRC3 = %s \n",dirc);
   }    }
     ss = strrchr( name, '.' );            /* find last / */
     if (ss >0){
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      ss++;
     for(jj=1; jj<= nlstate+ndeath; jj++){      strcpy(ext,ss);                     /* save extension */
      printf("%lf ",ps[ii][jj]);      l1= strlen( name);
    }      l2= strlen(ss)+1;
     printf("\n ");      strncpy( finame, name, l1-l2);
     }      finame[l1-l2]= 0;
     printf("\n ");printf("%lf ",cov[2]);*/    }
 /*  
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    return( 0 );                          /* we're done */
   goto end;*/  }
     return ps;  
 }  
   /******************************************/
 /**************** Product of 2 matrices ******************/  
   void replace_back_to_slash(char *s, char*t)
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  {
 {    int i;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    int lg=0;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    i=0;
   /* in, b, out are matrice of pointers which should have been initialized    lg=strlen(t);
      before: only the contents of out is modified. The function returns    for(i=0; i<= lg; i++) {
      a pointer to pointers identical to out */      (s[i] = t[i]);
   long i, j, k;      if (t[i]== '\\') s[i]='/';
   for(i=nrl; i<= nrh; i++)    }
     for(k=ncolol; k<=ncoloh; k++)  }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];  char *trimbb(char *out, char *in)
   { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
   return out;    char *s;
 }    s=out;
     while (*in != '\0'){
       while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
 /************* Higher Matrix Product ***************/        in++;
       }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      *out++ = *in++;
 {    }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    *out='\0';
      duration (i.e. until    return s;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  }
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  
      (typically every 2 years instead of every month which is too big).  char *cutl(char *blocc, char *alocc, char *in, char occ)
      Model is determined by parameters x and covariates have to be  {
      included manually here.    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
        and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
      */       gives blocc="abcdef2ghi" and alocc="j".
        If occ is not found blocc is null and alocc is equal to in. Returns blocc
   int i, j, d, h, k;    */
   double **out, cov[NCOVMAX];    char *s, *t;
   double **newm;    t=in;s=in;
     while ((*in != occ) && (*in != '\0')){
   /* Hstepm could be zero and should return the unit matrix */      *alocc++ = *in++;
   for (i=1;i<=nlstate+ndeath;i++)    }
     for (j=1;j<=nlstate+ndeath;j++){    if( *in == occ){
       oldm[i][j]=(i==j ? 1.0 : 0.0);      *(alocc)='\0';
       po[i][j][0]=(i==j ? 1.0 : 0.0);      s=++in;
     }    }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */   
   for(h=1; h <=nhstepm; h++){    if (s == t) {/* occ not found */
     for(d=1; d <=hstepm; d++){      *(alocc-(in-s))='\0';
       newm=savm;      in=s;
       /* Covariates have to be included here again */    }
       cov[1]=1.;    while ( *in != '\0'){
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      *blocc++ = *in++;
       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];    *blocc='\0';
       for (k=1; k<=cptcovprod;k++)    return t;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  }
   char *cutv(char *blocc, char *alocc, char *in, char occ)
   {
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,       gives blocc="abcdef2ghi" and alocc="j".
                    pmij(pmmij,cov,ncovmodel,x,nlstate));       If occ is not found blocc is null and alocc is equal to in. Returns alocc
       savm=oldm;    */
       oldm=newm;    char *s, *t;
     }    t=in;s=in;
     for(i=1; i<=nlstate+ndeath; i++)    while (*in != '\0'){
       for(j=1;j<=nlstate+ndeath;j++) {      while( *in == occ){
         po[i][j][h]=newm[i][j];        *blocc++ = *in++;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        s=in;
          */      }
       }      *blocc++ = *in++;
   } /* end h */    }
   return po;    if (s == t) /* occ not found */
 }      *(blocc-(in-s))='\0';
     else
       *(blocc-(in-s)-1)='\0';
 /*************** log-likelihood *************/    in=s;
 double func( double *x)    while ( *in != '\0'){
 {      *alocc++ = *in++;
   int i, ii, j, k, mi, d, kk;    }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;    *alocc='\0';
   double sw; /* Sum of weights */    return s;
   double lli; /* Individual log likelihood */  }
   long ipmx;  
   /*extern weight */  int nbocc(char *s, char occ)
   /* We are differentiating ll according to initial status */  {
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    int i,j=0;
   /*for(i=1;i<imx;i++)    int lg=20;
     printf(" %d\n",s[4][i]);    i=0;
   */    lg=strlen(s);
   cov[1]=1.;    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    }
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    return j;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  }
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)  /* void cutv(char *u,char *v, char*t, char occ) */
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /* { */
       for(d=0; d<dh[mi][i]; d++){  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
         newm=savm;  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  /*      gives u="abcdef2ghi" and v="j" *\/ */
         for (kk=1; kk<=cptcovage;kk++) {  /*   int i,lg,j,p=0; */
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  /*   i=0; */
         }  /*   lg=strlen(t); */
          /*   for(j=0; j<=lg-1; j++) { */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  /*   } */
         savm=oldm;  
         oldm=newm;  /*   for(j=0; j<p; j++) { */
          /*     (u[j] = t[j]); */
          /*   } */
       } /* end mult */  /*      u[p]='\0'; */
        
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  /*    for(j=0; j<= lg; j++) { */
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
       ipmx +=1;  /*   } */
       sw += weight[i];  /* } */
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */  #ifdef _WIN32
   } /* end of individual */  char * strsep(char **pp, const char *delim)
   {
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    char *p, *q;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */           
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    if ((p = *pp) == NULL)
   return -l;      return 0;
 }    if ((q = strpbrk (p, delim)) != NULL)
     {
       *pp = q + 1;
 /*********** Maximum Likelihood Estimation ***************/      *q = '\0';
     }
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    else
 {      *pp = 0;
   int i,j, iter;    return p;
   double **xi,*delti;  }
   double fret;  #endif
   xi=matrix(1,npar,1,npar);  
   for (i=1;i<=npar;i++)  /********************** nrerror ********************/
     for (j=1;j<=npar;j++)  
       xi[i][j]=(i==j ? 1.0 : 0.0);  void nrerror(char error_text[])
   printf("Powell\n");  fprintf(ficlog,"Powell\n");  {
   powell(p,xi,npar,ftol,&iter,&fret,func);    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    exit(EXIT_FAILURE);
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  }
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  /*********************** vector *******************/
   double *vector(int nl, int nh)
 }  {
     double *v;
 /**** Computes Hessian and covariance matrix ***/    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    if (!v) nrerror("allocation failure in vector");
 {    return v-nl+NR_END;
   double  **a,**y,*x,pd;  }
   double **hess;  
   int i, j,jk;  /************************ free vector ******************/
   int *indx;  void free_vector(double*v, int nl, int nh)
   {
   double hessii(double p[], double delta, int theta, double delti[]);    free((FREE_ARG)(v+nl-NR_END));
   double hessij(double p[], double delti[], int i, int j);  }
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  /************************ivector *******************************/
   int *ivector(long nl,long nh)
   hess=matrix(1,npar,1,npar);  {
     int *v;
   printf("\nCalculation of the hessian matrix. Wait...\n");    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");    if (!v) nrerror("allocation failure in ivector");
   for (i=1;i<=npar;i++){    return v-nl+NR_END;
     printf("%d",i);fflush(stdout);  }
     fprintf(ficlog,"%d",i);fflush(ficlog);  
     hess[i][i]=hessii(p,ftolhess,i,delti);  /******************free ivector **************************/
     /*printf(" %f ",p[i]);*/  void free_ivector(int *v, long nl, long nh)
     /*printf(" %lf ",hess[i][i]);*/  {
   }    free((FREE_ARG)(v+nl-NR_END));
    }
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++)  {  /************************lvector *******************************/
       if (j>i) {  long *lvector(long nl,long nh)
         printf(".%d%d",i,j);fflush(stdout);  {
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);    long *v;
         hess[i][j]=hessij(p,delti,i,j);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         hess[j][i]=hess[i][j];        if (!v) nrerror("allocation failure in ivector");
         /*printf(" %lf ",hess[i][j]);*/    return v-nl+NR_END;
       }  }
     }  
   }  /******************free lvector **************************/
   printf("\n");  void free_lvector(long *v, long nl, long nh)
   fprintf(ficlog,"\n");  {
     free((FREE_ARG)(v+nl-NR_END));
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  }
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");  
    /******************* imatrix *******************************/
   a=matrix(1,npar,1,npar);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   y=matrix(1,npar,1,npar);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   x=vector(1,npar);  { 
   indx=ivector(1,npar);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   for (i=1;i<=npar;i++)    int **m; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    
   ludcmp(a,npar,indx,&pd);    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   for (j=1;j<=npar;j++) {    if (!m) nrerror("allocation failure 1 in matrix()"); 
     for (i=1;i<=npar;i++) x[i]=0;    m += NR_END; 
     x[j]=1;    m -= nrl; 
     lubksb(a,npar,indx,x);    
     for (i=1;i<=npar;i++){    
       matcov[i][j]=x[i];    /* allocate rows and set pointers to them */ 
     }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
   printf("\n#Hessian matrix#\n");    m[nrl] -= ncl; 
   fprintf(ficlog,"\n#Hessian matrix#\n");    
   for (i=1;i<=npar;i++) {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     for (j=1;j<=npar;j++) {    
       printf("%.3e ",hess[i][j]);    /* return pointer to array of pointers to rows */ 
       fprintf(ficlog,"%.3e ",hess[i][j]);    return m; 
     }  } 
     printf("\n");  
     fprintf(ficlog,"\n");  /****************** free_imatrix *************************/
   }  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
   /* Recompute Inverse */        long nch,ncl,nrh,nrl; 
   for (i=1;i<=npar;i++)       /* free an int matrix allocated by imatrix() */ 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  { 
   ludcmp(a,npar,indx,&pd);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
   /*  printf("\n#Hessian matrix recomputed#\n");  } 
   
   for (j=1;j<=npar;j++) {  /******************* matrix *******************************/
     for (i=1;i<=npar;i++) x[i]=0;  double **matrix(long nrl, long nrh, long ncl, long nch)
     x[j]=1;  {
     lubksb(a,npar,indx,x);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     for (i=1;i<=npar;i++){    double **m;
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       fprintf(ficlog,"%.3e ",y[i][j]);    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
     printf("\n");    m -= nrl;
     fprintf(ficlog,"\n");  
   }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
   free_matrix(a,1,npar,1,npar);    m[nrl] -= ncl;
   free_matrix(y,1,npar,1,npar);  
   free_vector(x,1,npar);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   free_ivector(indx,1,npar);    return m;
   free_matrix(hess,1,npar,1,npar);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
 }     */
   }
 /*************** hessian matrix ****************/  
 double hessii( double x[], double delta, int theta, double delti[])  /*************************free matrix ************************/
 {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   int i;  {
   int l=1, lmax=20;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double k1,k2;    free((FREE_ARG)(m+nrl-NR_END));
   double p2[NPARMAX+1];  }
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  /******************* ma3x *******************************/
   double fx;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   int k=0,kmax=10;  {
   double l1;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
   fx=func(x);  
   for (i=1;i<=npar;i++) p2[i]=x[i];    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   for(l=0 ; l <=lmax; l++){    if (!m) nrerror("allocation failure 1 in matrix()");
     l1=pow(10,l);    m += NR_END;
     delts=delt;    m -= nrl;
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       p2[theta]=x[theta] +delt;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       k1=func(p2)-fx;    m[nrl] += NR_END;
       p2[theta]=x[theta]-delt;    m[nrl] -= ncl;
       k2=func(p2)-fx;  
       /*res= (k1-2.0*fx+k2)/delt/delt; */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  
          m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 #ifdef DEBUG    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    m[nrl][ncl] += NR_END;
       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);    m[nrl][ncl] -= nll;
 #endif    for (j=ncl+1; j<=nch; j++) 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      m[nrl][j]=m[nrl][j-1]+nlay;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    
         k=kmax;    for (i=nrl+1; i<=nrh; i++) {
       }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      for (j=ncl+1; j<=nch; j++) 
         k=kmax; l=lmax*10.;        m[i][j]=m[i][j-1]+nlay;
       }    }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    return m; 
         delts=delt;    /*  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)
     }    */
   }  }
   delti[theta]=delts;  
   return res;  /*************************free ma3x ************************/
    void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 }  {
     free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 double hessij( double x[], double delti[], int thetai,int thetaj)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 {    free((FREE_ARG)(m+nrl-NR_END));
   int i;  }
   int l=1, l1, lmax=20;  
   double k1,k2,k3,k4,res,fx;  /*************** function subdirf ***********/
   double p2[NPARMAX+1];  char *subdirf(char fileres[])
   int k;  {
     /* Caution optionfilefiname is hidden */
   fx=func(x);    strcpy(tmpout,optionfilefiname);
   for (k=1; k<=2; k++) {    strcat(tmpout,"/"); /* Add to the right */
     for (i=1;i<=npar;i++) p2[i]=x[i];    strcat(tmpout,fileres);
     p2[thetai]=x[thetai]+delti[thetai]/k;    return tmpout;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  }
     k1=func(p2)-fx;  
    /*************** function subdirf2 ***********/
     p2[thetai]=x[thetai]+delti[thetai]/k;  char *subdirf2(char fileres[], char *preop)
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  {
     k2=func(p2)-fx;    
      /* Caution optionfilefiname is hidden */
     p2[thetai]=x[thetai]-delti[thetai]/k;    strcpy(tmpout,optionfilefiname);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    strcat(tmpout,"/");
     k3=func(p2)-fx;    strcat(tmpout,preop);
      strcat(tmpout,fileres);
     p2[thetai]=x[thetai]-delti[thetai]/k;    return tmpout;
     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 subdirf3 ***********/
 #ifdef DEBUG  char *subdirf3(char fileres[], char *preop, char *preop2)
     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    /* Caution optionfilefiname is hidden */
   }    strcpy(tmpout,optionfilefiname);
   return res;    strcat(tmpout,"/");
 }    strcat(tmpout,preop);
     strcat(tmpout,preop2);
 /************** Inverse of matrix **************/    strcat(tmpout,fileres);
 void ludcmp(double **a, int n, int *indx, double *d)    return tmpout;
 {  }
   int i,imax,j,k;  
   double big,dum,sum,temp;  char *asc_diff_time(long time_sec, char ascdiff[])
   double *vv;  {
      long sec_left, days, hours, minutes;
   vv=vector(1,n);    days = (time_sec) / (60*60*24);
   *d=1.0;    sec_left = (time_sec) % (60*60*24);
   for (i=1;i<=n;i++) {    hours = (sec_left) / (60*60) ;
     big=0.0;    sec_left = (sec_left) %(60*60);
     for (j=1;j<=n;j++)    minutes = (sec_left) /60;
       if ((temp=fabs(a[i][j])) > big) big=temp;    sec_left = (sec_left) % (60);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
     vv[i]=1.0/big;    return ascdiff;
   }  }
   for (j=1;j<=n;j++) {  
     for (i=1;i<j;i++) {  /***************** f1dim *************************/
       sum=a[i][j];  extern int ncom; 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  extern double *pcom,*xicom;
       a[i][j]=sum;  extern double (*nrfunc)(double []); 
     }   
     big=0.0;  double f1dim(double x) 
     for (i=j;i<=n;i++) {  { 
       sum=a[i][j];    int j; 
       for (k=1;k<j;k++)    double f;
         sum -= a[i][k]*a[k][j];    double *xt; 
       a[i][j]=sum;   
       if ( (dum=vv[i]*fabs(sum)) >= big) {    xt=vector(1,ncom); 
         big=dum;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
         imax=i;    f=(*nrfunc)(xt); 
       }    free_vector(xt,1,ncom); 
     }    return f; 
     if (j != imax) {  } 
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];  /*****************brent *************************/
         a[imax][k]=a[j][k];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         a[j][k]=dum;  { 
       }    int iter; 
       *d = -(*d);    double a,b,d,etemp;
       vv[imax]=vv[j];    double fu=0,fv,fw,fx;
     }    double ftemp=0.;
     indx[j]=imax;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     if (a[j][j] == 0.0) a[j][j]=TINY;    double e=0.0; 
     if (j != n) {   
       dum=1.0/(a[j][j]);    a=(ax < cx ? ax : cx); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    b=(ax > cx ? ax : cx); 
     }    x=w=v=bx; 
   }    fw=fv=fx=(*f)(x); 
   free_vector(vv,1,n);  /* Doesn't work */    for (iter=1;iter<=ITMAX;iter++) { 
 ;      xm=0.5*(a+b); 
 }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 void lubksb(double **a, int n, int *indx, double b[])      printf(".");fflush(stdout);
 {      fprintf(ficlog,".");fflush(ficlog);
   int i,ii=0,ip,j;  #ifdef DEBUGBRENT
   double sum;      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
        fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   for (i=1;i<=n;i++) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     ip=indx[i];  #endif
     sum=b[ip];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     b[ip]=b[i];        *xmin=x; 
     if (ii)        return fx; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];      } 
     else if (sum) ii=i;      ftemp=fu;
     b[i]=sum;      if (fabs(e) > tol1) { 
   }        r=(x-w)*(fx-fv); 
   for (i=n;i>=1;i--) {        q=(x-v)*(fx-fw); 
     sum=b[i];        p=(x-v)*q-(x-w)*r; 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        q=2.0*(q-r); 
     b[i]=sum/a[i][i];        if (q > 0.0) p = -p; 
   }        q=fabs(q); 
 }        etemp=e; 
         e=d; 
 /************ Frequencies ********************/        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 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)          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 {  /* Some frequencies */        else { 
            d=p/q; 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          u=x+d; 
   int first;          if (u-a < tol2 || b-u < tol2) 
   double ***freq; /* Frequencies */            d=SIGN(tol1,xm-x); 
   double *pp;        } 
   double pos, k2, dateintsum=0,k2cpt=0;      } else { 
   FILE *ficresp;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   char fileresp[FILENAMELENGTH];      } 
        u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   pp=vector(1,nlstate);      fu=(*f)(u); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (fu <= fx) { 
   strcpy(fileresp,"p");        if (u >= x) a=x; else b=x; 
   strcat(fileresp,fileres);        SHFT(v,w,x,u) 
   if((ficresp=fopen(fileresp,"w"))==NULL) {          SHFT(fv,fw,fx,fu) 
     printf("Problem with prevalence resultfile: %s\n", fileresp);          } else { 
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);            if (u < x) a=u; else b=u; 
     exit(0);            if (fu <= fw || w == x) { 
   }              v=w; 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);              w=u; 
   j1=0;              fv=fw; 
                fw=fu; 
   j=cptcoveff;            } else if (fu <= fv || v == x || v == w) { 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}              v=u; 
               fv=fu; 
   first=1;            } 
           } 
   for(k1=1; k1<=j;k1++){    } 
     for(i1=1; i1<=ncodemax[k1];i1++){    nrerror("Too many iterations in brent"); 
       j1++;    *xmin=x; 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    return fx; 
         scanf("%d", i);*/  } 
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)    /****************** mnbrak ***********************/
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
                    double (*func)(double)) 
       dateintsum=0;  { 
       k2cpt=0;    double ulim,u,r,q, dum;
       for (i=1; i<=imx; i++) {    double fu; 
         bool=1;   
         if  (cptcovn>0) {    *fa=(*func)(*ax); 
           for (z1=1; z1<=cptcoveff; z1++)    *fb=(*func)(*bx); 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    if (*fb > *fa) { 
               bool=0;      SHFT(dum,*ax,*bx,dum) 
         }        SHFT(dum,*fb,*fa,dum) 
         if (bool==1) {        } 
           for(m=firstpass; m<=lastpass; m++){    *cx=(*bx)+GOLD*(*bx-*ax); 
             k2=anint[m][i]+(mint[m][i]/12.);    *fc=(*func)(*cx); 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    while (*fb > *fc) { /* Declining fa, fb, fc */
               if(agev[m][i]==0) agev[m][i]=agemax+1;      r=(*bx-*ax)*(*fb-*fc); 
               if(agev[m][i]==1) agev[m][i]=agemax+2;      q=(*bx-*cx)*(*fb-*fa); 
               if (m<lastpass) {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
               }      if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
                      fu=(*func)(u); 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  #ifdef DEBUG
                 dateintsum=dateintsum+k2;        /* f(x)=A(x-u)**2+f(u) */
                 k2cpt++;        double A, fparabu; 
               }        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
             }        fparabu= *fa - A*(*ax-u)*(*ax-u);
           }        printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
         }        fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
       }  #endif 
              } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        fu=(*func)(u); 
         if (fu < *fc) { 
       if  (cptcovn>0) {          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         fprintf(ficresp, "\n#********** Variable ");            SHFT(*fb,*fc,fu,(*func)(u)) 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            } 
         fprintf(ficresp, "**********\n#");      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
       }        u=ulim; 
       for(i=1; i<=nlstate;i++)        fu=(*func)(u); 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      } else { 
       fprintf(ficresp, "\n");        u=(*cx)+GOLD*(*cx-*bx); 
              fu=(*func)(u); 
       for(i=(int)agemin; i <= (int)agemax+3; i++){      } 
         if(i==(int)agemax+3){      SHFT(*ax,*bx,*cx,u) 
           fprintf(ficlog,"Total");        SHFT(*fa,*fb,*fc,fu) 
         }else{        } 
           if(first==1){  } 
             first=0;  
             printf("See log file for details...\n");  /*************** linmin ************************/
           }  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
           fprintf(ficlog,"Age %d", i);  resets p to where the function func(p) takes on a minimum along the direction xi from p ,
         }  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
         for(jk=1; jk <=nlstate ; jk++){  the value of func at the returned location p . This is actually all accomplished by calling the
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  routines mnbrak and brent .*/
             pp[jk] += freq[jk][m][i];  int ncom; 
         }  double *pcom,*xicom;
         for(jk=1; jk <=nlstate ; jk++){  double (*nrfunc)(double []); 
           for(m=-1, pos=0; m <=0 ; m++)   
             pos += freq[jk][m][i];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
           if(pp[jk]>=1.e-10){  { 
             if(first==1){    double brent(double ax, double bx, double cx, 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);                 double (*f)(double), double tol, double *xmin); 
             }    double f1dim(double x); 
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
           }else{                double *fc, double (*func)(double)); 
             if(first==1)    int j; 
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    double xx,xmin,bx,ax; 
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    double fx,fb,fa;
           }   
         }    ncom=n; 
     pcom=vector(1,n); 
         for(jk=1; jk <=nlstate ; jk++){    xicom=vector(1,n); 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    nrfunc=func; 
             pp[jk] += freq[jk][m][i];    for (j=1;j<=n;j++) { 
         }      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
         for(jk=1,pos=0; jk <=nlstate ; jk++)    } 
           pos += pp[jk];    ax=0.0; 
         for(jk=1; jk <=nlstate ; jk++){    xx=1.0; 
           if(pos>=1.e-5){    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
             if(first==1)    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  #ifdef DEBUG
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
           }else{    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
             if(first==1)  #endif
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    for (j=1;j<=n;j++) { 
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      xi[j] *= xmin; 
           }      p[j] += xi[j]; 
           if( i <= (int) agemax){    } 
             if(pos>=1.e-5){    free_vector(xicom,1,n); 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    free_vector(pcom,1,n); 
               probs[i][jk][j1]= pp[jk]/pos;  } 
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  
             }  
             else  /*************** powell ************************/
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  /*
           }  Minimization of a function func of n variables. Input consists of an initial starting point
         }  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
          rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
         for(jk=-1; jk <=nlstate+ndeath; jk++)  such that failure to decrease by more than this amount on one iteration signals doneness. On
           for(m=-1; m <=nlstate+ndeath; m++)  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
             if(freq[jk][m][i] !=0 ) {  function value at p , and iter is the number of iterations taken. The routine linmin is used.
             if(first==1)   */
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);              double (*func)(double [])) 
             }  { 
         if(i <= (int) agemax)    void linmin(double p[], double xi[], int n, double *fret, 
           fprintf(ficresp,"\n");                double (*func)(double [])); 
         if(first==1)    int i,ibig,j; 
           printf("Others in log...\n");    double del,t,*pt,*ptt,*xit;
         fprintf(ficlog,"\n");    double fp,fptt;
       }    double *xits;
     }    int niterf, itmp;
   }  
   dateintmean=dateintsum/k2cpt;    pt=vector(1,n); 
      ptt=vector(1,n); 
   fclose(ficresp);    xit=vector(1,n); 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    xits=vector(1,n); 
   free_vector(pp,1,nlstate);    *fret=(*func)(p); 
      for (j=1;j<=n;j++) pt[j]=p[j]; 
   /* End of Freq */      rcurr_time = time(NULL);  
 }    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
 /************ Prevalence ********************/      ibig=0; 
 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)      del=0.0; 
 {  /* Some frequencies */      rlast_time=rcurr_time;
        /* (void) gettimeofday(&curr_time,&tzp); */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      rcurr_time = time(NULL);  
   double ***freq; /* Frequencies */      curr_time = *localtime(&rcurr_time);
   double *pp;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
   double pos, k2;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
   /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
   pp=vector(1,nlstate);     for (i=1;i<=n;i++) {
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        printf(" %d %.12f",i, p[i]);
          fprintf(ficlog," %d %.12lf",i, p[i]);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        fprintf(ficrespow," %.12lf", p[i]);
   j1=0;      }
        printf("\n");
   j=cptcoveff;      fprintf(ficlog,"\n");
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      fprintf(ficrespow,"\n");fflush(ficrespow);
        if(*iter <=3){
   for(k1=1; k1<=j;k1++){        tml = *localtime(&rcurr_time);
     for(i1=1; i1<=ncodemax[k1];i1++){        strcpy(strcurr,asctime(&tml));
       j1++;        rforecast_time=rcurr_time; 
              itmp = strlen(strcurr);
       for (i=-1; i<=nlstate+ndeath; i++)          if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         for (jk=-1; jk<=nlstate+ndeath; jk++)            strcurr[itmp-1]='\0';
           for(m=agemin; m <= agemax+3; m++)        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
             freq[i][jk][m]=0;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
              for(niterf=10;niterf<=30;niterf+=10){
       for (i=1; i<=imx; i++) {          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         bool=1;          forecast_time = *localtime(&rforecast_time);
         if  (cptcovn>0) {          strcpy(strfor,asctime(&forecast_time));
           for (z1=1; z1<=cptcoveff; z1++)          itmp = strlen(strfor);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          if(strfor[itmp-1]=='\n')
               bool=0;          strfor[itmp-1]='\0';
         }          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
         if (bool==1) {          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
           for(m=firstpass; m<=lastpass; m++){        }
             k2=anint[m][i]+(mint[m][i]/12.);      }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      for (i=1;i<=n;i++) { 
               if(agev[m][i]==0) agev[m][i]=agemax+1;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
               if(agev[m][i]==1) agev[m][i]=agemax+2;        fptt=(*fret); 
               if (m<lastpass) {  #ifdef DEBUG
                 if (calagedate>0)            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
                 else  #endif
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        printf("%d",i);fflush(stdout);
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];        fprintf(ficlog,"%d",i);fflush(ficlog);
               }        linmin(p,xit,n,fret,func); 
             }        if (fabs(fptt-(*fret)) > del) { 
           }          del=fabs(fptt-(*fret)); 
         }          ibig=i; 
       }        } 
       for(i=(int)agemin; i <= (int)agemax+3; i++){  #ifdef DEBUG
         for(jk=1; jk <=nlstate ; jk++){        printf("%d %.12e",i,(*fret));
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        fprintf(ficlog,"%d %.12e",i,(*fret));
             pp[jk] += freq[jk][m][i];        for (j=1;j<=n;j++) {
         }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         for(jk=1; jk <=nlstate ; jk++){          printf(" x(%d)=%.12e",j,xit[j]);
           for(m=-1, pos=0; m <=0 ; m++)          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
             pos += freq[jk][m][i];        }
         }        for(j=1;j<=n;j++) {
                  printf(" p(%d)=%.12e",j,p[j]);
         for(jk=1; jk <=nlstate ; jk++){          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        }
             pp[jk] += freq[jk][m][i];        printf("\n");
         }        fprintf(ficlog,"\n");
          #endif
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      } /* end i */
              if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         for(jk=1; jk <=nlstate ; jk++){      #ifdef DEBUG
           if( i <= (int) agemax){        int k[2],l;
             if(pos>=1.e-5){        k[0]=1;
               probs[i][jk][j1]= pp[jk]/pos;        k[1]=-1;
             }        printf("Max: %.12e",(*func)(p));
           }        fprintf(ficlog,"Max: %.12e",(*func)(p));
         }/* end jk */        for (j=1;j<=n;j++) {
       }/* end i */          printf(" %.12e",p[j]);
     } /* end i1 */          fprintf(ficlog," %.12e",p[j]);
   } /* end k1 */        }
         printf("\n");
          fprintf(ficlog,"\n");
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        for(l=0;l<=1;l++) {
   free_vector(pp,1,nlstate);          for (j=1;j<=n;j++) {
              ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 }  /* End of Freq */            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
             fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 /************* Waves Concatenation ***************/          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 {        }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  #endif
      Death is a valid wave (if date is known).  
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        free_vector(xit,1,n); 
      and mw[mi+1][i]. dh depends on stepm.        free_vector(xits,1,n); 
      */        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
   int i, mi, m;        return; 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      } 
      double sum=0., jmean=0.;*/      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   int first;      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
   int j, k=0,jk, ju, jl;        ptt[j]=2.0*p[j]-pt[j]; 
   double sum=0.;        xit[j]=p[j]-pt[j]; 
   first=0;        pt[j]=p[j]; 
   jmin=1e+5;      } 
   jmax=-1;      fptt=(*func)(ptt); 
   jmean=0.;      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
   for(i=1; i<=imx; i++){        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
     mi=0;        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
     m=firstpass;        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
     while(s[m][i] <= nlstate){        /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
       if(s[m][i]>=1)        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
         mw[++mi][i]=m;        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
       if(m >=lastpass)        /* Thus we compare delta(2h) with observed f1-f3 */
         break;        /* or best gain on one ancient line 'del' with total  */
       else        /* gain f1-f2 = f1 - f2 - 'del' with del  */
         m++;        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
     }/* end while */  
     if (s[m][i] > nlstate){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
       mi++;     /* Death is another wave */        t= t- del*SQR(fp-fptt);
       /* if(mi==0)  never been interviewed correctly before death */        printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
          /* Only death is a correct wave */        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);
       mw[mi][i]=m;  #ifdef DEBUG
     }        printf("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));
     wav[i]=mi;        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
     if(mi==0){               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
       if(first==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);
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);        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);
         first=1;  #endif
       }        if (t < 0.0) { /* Then we use it for last direction */
       if(first==1){          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);          for (j=1;j<=n;j++) { 
       }            xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
     } /* end mi==0 */            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
   }          }
           printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   for(i=1; i<=imx; i++){          fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
     for(mi=1; mi<wav[i];mi++){  
       if (stepm <=0)  #ifdef DEBUG
         dh[mi][i]=1;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       else{          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         if (s[mw[mi+1][i]][i] > nlstate) {          for(j=1;j<=n;j++){
           if (agedc[i] < 2*AGESUP) {            printf(" %.12e",xit[j]);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);            fprintf(ficlog," %.12e",xit[j]);
           if(j==0) j=1;  /* Survives at least one month after exam */          }
           k=k+1;          printf("\n");
           if (j >= jmax) jmax=j;          fprintf(ficlog,"\n");
           if (j <= jmin) jmin=j;  #endif
           sum=sum+j;        } /* end of t negative */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      } /* end if (fptt < fp)  */
           }    } 
         }  } 
         else{  
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  /**** Prevalence limit (stable or period prevalence)  ****************/
           k=k+1;  
           if (j >= jmax) jmax=j;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
           else if (j <= jmin)jmin=j;  {
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
           sum=sum+j;       matrix by transitions matrix until convergence is reached */
         }    
         jk= j/stepm;    int i, ii,j,k;
         jl= j -jk*stepm;    double min, max, maxmin, maxmax,sumnew=0.;
         ju= j -(jk+1)*stepm;    /* double **matprod2(); */ /* test */
         if(jl <= -ju)    double **out, cov[NCOVMAX+1], **pmij();
           dh[mi][i]=jk;    double **newm;
         else    double agefin, delaymax=50 ; /* Max number of years to converge */
           dh[mi][i]=jk+1;    
         if(dh[mi][i]==0)    for (ii=1;ii<=nlstate+ndeath;ii++)
           dh[mi][i]=1; /* At least one step */      for (j=1;j<=nlstate+ndeath;j++){
       }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }      }
   }    
   jmean=sum/k;    cov[1]=1.;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
  }    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
 /*********** Tricode ****************************/      /* Covariates have to be included here again */
 void tricode(int *Tvar, int **nbcode, int imx)      cov[2]=agefin;
 {      
   int Ndum[20],ij=1, k, j, i;      for (k=1; k<=cptcovn;k++) {
   int cptcode=0;        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   cptcoveff=0;        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
        }
   for (k=0; k<19; k++) Ndum[k]=0;      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   for (k=1; k<=7; k++) ncodemax[k]=0;      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
       /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      
     for (i=1; i<=imx; i++) {      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       ij=(int)(covar[Tvar[j]][i]);      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       Ndum[ij]++;      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
       if (ij > cptcode) cptcode=ij;      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
     }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
       
     for (i=0; i<=cptcode; i++) {      savm=oldm;
       if(Ndum[i]!=0) ncodemax[j]++;      oldm=newm;
     }      maxmax=0.;
     ij=1;      for(j=1;j<=nlstate;j++){
         min=1.;
         max=0.;
     for (i=1; i<=ncodemax[j]; i++) {        for(i=1; i<=nlstate; i++) {
       for (k=0; k<=19; k++) {          sumnew=0;
         if (Ndum[k] != 0) {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           nbcode[Tvar[j]][ij]=k;          prlim[i][j]= newm[i][j]/(1-sumnew);
                    /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
           ij++;          max=FMAX(max,prlim[i][j]);
         }          min=FMIN(min,prlim[i][j]);
         if (ij > ncodemax[j]) break;        }
       }          maxmin=max-min;
     }        maxmax=FMAX(maxmax,maxmin);
   }        } /* j loop */
       if(maxmax < ftolpl){
  for (k=0; k<19; k++) Ndum[k]=0;        return prlim;
       }
  for (i=1; i<=ncovmodel-2; i++) {    } /* age loop */
    ij=Tvar[i];    return prlim; /* should not reach here */
    Ndum[ij]++;  }
  }  
   /*************** transition probabilities ***************/ 
  ij=1;  
  for (i=1; i<=10; i++) {  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
    if((Ndum[i]!=0) && (i<=ncovcol)){  {
      Tvaraff[ij]=i;    /* According to parameters values stored in x and the covariate's values stored in cov,
      ij++;       computes the probability to be observed in state j being in state i by appying the
    }       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]
         and, according on how parameters are entered, the position of the coefficient xij(nc) of the
  cptcoveff=ij-1;       ncth covariate in the global vector x is given by the formula:
 }       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
        j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
 /*********** Health Expectancies ****************/       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
        sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
 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 )       Outputs ps[i][j] the probability to be observed in j being in j according to
        the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
 {    */
   /* Health expectancies */    double s1, lnpijopii;
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    /*double t34;*/
   double age, agelim, hf;    int i,j, nc, ii, jj;
   double ***p3mat,***varhe;  
   double **dnewm,**doldm;      for(i=1; i<= nlstate; i++){
   double *xp;        for(j=1; j<i;j++){
   double **gp, **gm;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   double ***gradg, ***trgradg;            /*lnpijopii += param[i][j][nc]*cov[nc];*/
   int theta;            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
   /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          }
   xp=vector(1,npar);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   dnewm=matrix(1,nlstate*2,1,npar);  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   doldm=matrix(1,nlstate*2,1,nlstate*2);        }
          for(j=i+1; j<=nlstate+ndeath;j++){
   fprintf(ficreseij,"# Health expectancies\n");          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
   fprintf(ficreseij,"# Age");            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
   for(i=1; i<=nlstate;i++)            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
     for(j=1; j<=nlstate;j++)  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          }
   fprintf(ficreseij,"\n");          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         }
   if(estepm < stepm){      }
     printf ("Problem %d lower than %d\n",estepm, stepm);      
   }      for(i=1; i<= nlstate; i++){
   else  hstepm=estepm;          s1=0;
   /* We compute the life expectancy from trapezoids spaced every estepm months        for(j=1; j<i; j++){
    * This is mainly to measure the difference between two models: for example          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
    * if stepm=24 months pijx are given only every 2 years and by summing them          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
    * we are calculating an estimate of the Life Expectancy assuming a linear        }
    * progression inbetween and thus overestimating or underestimating according        for(j=i+1; j<=nlstate+ndeath; j++){
    * to the curvature of the survival function. If, for the same date, we          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
    * estimate the model with stepm=1 month, we can keep estepm to 24 months          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
    * to compare the new estimate of Life expectancy with the same linear        }
    * hypothesis. A more precise result, taking into account a more precise        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
    * curvature will be obtained if estepm is as small as stepm. */        ps[i][i]=1./(s1+1.);
         /* Computing other pijs */
   /* For example we decided to compute the life expectancy with the smallest unit */        for(j=1; j<i; j++)
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          ps[i][j]= exp(ps[i][j])*ps[i][i];
      nhstepm is the number of hstepm from age to agelim        for(j=i+1; j<=nlstate+ndeath; j++)
      nstepm is the number of stepm from age to agelin.          ps[i][j]= exp(ps[i][j])*ps[i][i];
      Look at hpijx to understand the reason of that which relies in memory size        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
      and note for a fixed period like estepm months */      } /* end i */
   /* 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(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
      means that if the survival funtion is printed only each two years of age and if        for(jj=1; jj<= nlstate+ndeath; jj++){
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          ps[ii][jj]=0;
      results. So we changed our mind and took the option of the best precision.          ps[ii][ii]=1;
   */        }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      }
       
   agelim=AGESUP;      
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
     /* nhstepm age range expressed in number of stepm */      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */      /*   } */
     /* if (stepm >= YEARM) hstepm=1;*/      /*   printf("\n "); */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      /* } */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* printf("\n ");printf("%lf ",cov[2]);*/
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);      /*
     gp=matrix(0,nhstepm,1,nlstate*2);        for(i=1; i<= npar; i++) printf("%f ",x[i]);
     gm=matrix(0,nhstepm,1,nlstate*2);        goto end;*/
       return ps;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    /**************** Product of 2 matrices ******************/
    
   double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     /* Computing Variances of health expectancies */       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
      for(theta=1; theta <=npar; theta++){       before: only the contents of out is modified. The function returns
       for(i=1; i<=npar; i++){       a pointer to pointers identical to out */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    int i, j, k;
       }    for(i=nrl; i<= nrh; i++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for(k=ncolol; k<=ncoloh; k++){
          out[i][k]=0.;
       cptj=0;        for(j=ncl; j<=nch; j++)
       for(j=1; j<= nlstate; j++){          out[i][k] +=in[i][j]*b[j][k];
         for(i=1; i<=nlstate; i++){      }
           cptj=cptj+1;    return out;
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){  }
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }  
         }  /************* Higher Matrix Product ***************/
       }  
        double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
        {
       for(i=1; i<=npar; i++)    /* Computes the transition matrix starting at age 'age' over 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       'nhstepm*hstepm*stepm' months (i.e. until
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);         age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
             nhstepm*hstepm matrices. 
       cptj=0;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       for(j=1; j<= nlstate; j++){       (typically every 2 years instead of every month which is too big 
         for(i=1;i<=nlstate;i++){       for the memory).
           cptj=cptj+1;       Model is determined by parameters x and covariates have to be 
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){       included manually here. 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }       */
         }  
       }    int i, j, d, h, k;
       for(j=1; j<= nlstate*2; j++)    double **out, cov[NCOVMAX+1];
         for(h=0; h<=nhstepm-1; h++){    double **newm;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }    /* Hstepm could be zero and should return the unit matrix */
      }    for (i=1;i<=nlstate+ndeath;i++)
          for (j=1;j<=nlstate+ndeath;j++){
 /* End theta */        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
      for(h=0; h<=nhstepm-1; h++)    for(h=1; h <=nhstepm; h++){
       for(j=1; j<=nlstate*2;j++)      for(d=1; d <=hstepm; d++){
         for(theta=1; theta <=npar; theta++)        newm=savm;
           trgradg[h][j][theta]=gradg[h][theta][j];        /* Covariates have to be included here again */
              cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
      for(i=1;i<=nlstate*2;i++)        for (k=1; k<=cptcovn;k++) 
       for(j=1;j<=nlstate*2;j++)          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         varhe[i][j][(int)age] =0.;        for (k=1; k<=cptcovage;k++)
           cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      printf("%d|",(int)age);fflush(stdout);        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      for(h=0;h<=nhstepm-1;h++){  
       for(k=0;k<=nhstepm-1;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         for(i=1;i<=nlstate*2;i++)        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
           for(j=1;j<=nlstate*2;j++)                     pmij(pmmij,cov,ncovmodel,x,nlstate));
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;        savm=oldm;
       }        oldm=newm;
     }      }
     /* Computing expectancies */      for(i=1; i<=nlstate+ndeath; i++)
     for(i=1; i<=nlstate;i++)        for(j=1;j<=nlstate+ndeath;j++) {
       for(j=1; j<=nlstate;j++)          po[i][j][h]=newm[i][j];
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        }
                /*printf("h=%d ",h);*/
 /* 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]);*/    } /* end h */
   /*     printf("\n H=%d \n",h); */
         }    return po;
   }
     fprintf(ficreseij,"%3.0f",age );  
     cptj=0;  #ifdef NLOPT
     for(i=1; i<=nlstate;i++)    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
       for(j=1; j<=nlstate;j++){    double fret;
         cptj++;    double *xt;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );    int j;
       }    myfunc_data *d2 = (myfunc_data *) pd;
     fprintf(ficreseij,"\n");  /* xt = (p1-1); */
        xt=vector(1,n); 
     free_matrix(gm,0,nhstepm,1,nlstate*2);    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
     free_matrix(gp,0,nhstepm,1,nlstate*2);  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("Function = %.12lf ",fret);
   }    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
   printf("\n");    printf("\n");
   fprintf(ficlog,"\n");   free_vector(xt,1,n);
     return fret;
   free_vector(xp,1,npar);  }
   free_matrix(dnewm,1,nlstate*2,1,npar);  #endif
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);  /*************** log-likelihood *************/
 }  double func( double *x)
   {
 /************ Variance ******************/    int i, ii, j, k, mi, d, kk;
 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)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
 {    double **out;
   /* Variance of health expectancies */    double sw; /* Sum of weights */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double lli; /* Individual log likelihood */
   /* double **newm;*/    int s1, s2;
   double **dnewm,**doldm;    double bbh, survp;
   double **dnewmp,**doldmp;    long ipmx;
   int i, j, nhstepm, hstepm, h, nstepm ;    /*extern weight */
   int k, cptcode;    /* We are differentiating ll according to initial status */
   double *xp;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double **gp, **gm;  /* for var eij */    /*for(i=1;i<imx;i++) 
   double ***gradg, ***trgradg; /*for var eij */      printf(" %d\n",s[4][i]);
   double **gradgp, **trgradgp; /* for var p point j */    */
   double *gpp, *gmp; /* for var p point j */  
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */    ++countcallfunc;
   double ***p3mat;  
   double age,agelim, hf;    cov[1]=1.;
   int theta;  
   char digit[4];    for(k=1; k<=nlstate; k++) ll[k]=0.;
   char digitp[16];  
     if(mle==1){
   char fileresprobmorprev[FILENAMELENGTH];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         /* Computes the values of the ncovmodel covariates of the model
   if(popbased==1)           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
     strcpy(digitp,"-populbased-");           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
   else           to be observed in j being in i according to the model.
     strcpy(digitp,"-stablbased-");         */
         for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
   strcpy(fileresprobmorprev,"prmorprev");          cov[2+k]=covar[Tvar[k]][i];
   sprintf(digit,"%-d",ij);        }
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
   strcat(fileresprobmorprev,digit); /* Tvar to be done */           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
   strcat(fileresprobmorprev,digitp); /* Popbased or not */           has been calculated etc */
   strcat(fileresprobmorprev,fileres);        for(mi=1; mi<= wav[i]-1; mi++){
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     printf("Problem with resultfile: %s\n", fileresprobmorprev);            for (j=1;j<=nlstate+ndeath;j++){
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);            }
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);          for(d=0; d<dh[mi][i]; d++){
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");            newm=savm;
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){            for (kk=1; kk<=cptcovage;kk++) {
     fprintf(ficresprobmorprev," p.%-d SE",j);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
     for(i=1; i<=nlstate;i++)            }
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fprintf(ficresprobmorprev,"\n");            savm=oldm;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {            oldm=newm;
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);          } /* end mult */
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);        
     exit(0);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   }          /* But now since version 0.9 we anticipate for bias at large stepm.
   else{           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     fprintf(ficgp,"\n# Routine varevsij");           * (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
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     printf("Problem with html file: %s\n", optionfilehtm);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);           * probability in order to take into account the bias as a fraction of the way
     exit(0);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   }           * -stepm/2 to stepm/2 .
   else{           * For stepm=1 the results are the same as for previous versions of Imach.
     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");           * For stepm > 1 the results are less biased than in previous versions. 
   }           */
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   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");          bbh=(double)bh[mi][i]/(double)stepm; 
   fprintf(ficresvij,"# Age");          /* bias bh is positive if real duration
   for(i=1; i<=nlstate;i++)           * is higher than the multiple of stepm and negative otherwise.
     for(j=1; j<=nlstate;j++)           */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   fprintf(ficresvij,"\n");          if( s2 > nlstate){ 
             /* i.e. if s2 is a death state and if the date of death is known 
   xp=vector(1,npar);               then the contribution to the likelihood is the probability to 
   dnewm=matrix(1,nlstate,1,npar);               die between last step unit time and current  step unit time, 
   doldm=matrix(1,nlstate,1,nlstate);               which is also equal to probability to die before dh 
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);               minus probability to die before dh-stepm . 
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);          health state: the date of the interview describes the actual state
   gpp=vector(nlstate+1,nlstate+ndeath);          and not the date of a change in health state. The former idea was
   gmp=vector(nlstate+1,nlstate+ndeath);          to consider that at each interview the state was recorded
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/          (healthy, disable or death) and IMaCh was corrected; but when we
            introduced the exact date of death then we should have modified
   if(estepm < stepm){          the contribution of an exact death to the likelihood. This new
     printf ("Problem %d lower than %d\n",estepm, stepm);          contribution is smaller and very dependent of the step unit
   }          stepm. It is no more the probability to die between last interview
   else  hstepm=estepm;            and month of death but the probability to survive from last
   /* For example we decided to compute the life expectancy with the smallest unit */          interview up to one month before death multiplied by the
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          probability to die within a month. Thanks to Chris
      nhstepm is the number of hstepm from age to agelim          Jackson for correcting this bug.  Former versions increased
      nstepm is the number of stepm from age to agelin.          mortality artificially. The bad side is that we add another loop
      Look at hpijx to understand the reason of that which relies in memory size          which slows down the processing. The difference can be up to 10%
      and note for a fixed period like k years */          lower mortality.
   /* 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            lli=log(out[s1][s2] - savm[s1][s2]);
      means that if the survival funtion is printed only each two years of age and if  
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  
      results. So we changed our mind and took the option of the best precision.          } else if  (s2==-2) {
   */            for (j=1,survp=0. ; j<=nlstate; j++) 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   agelim = AGESUP;            /*survp += out[s1][j]; */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            lli= log(survp);
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          }
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          else if  (s2==-4) { 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);            for (j=3,survp=0. ; j<=nlstate; j++)  
     gp=matrix(0,nhstepm,1,nlstate);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     gm=matrix(0,nhstepm,1,nlstate);            lli= log(survp); 
           } 
   
     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); 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          
           else{
       if (popbased==1) {            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         for(i=1; i<=nlstate;i++)            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           prlim[i][i]=probs[(int)age][i][ij];          } 
       }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
            /*if(lli ==000.0)*/
       for(j=1; j<= nlstate; j++){          /*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); */
         for(h=0; h<=nhstepm; h++){          ipmx +=1;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          sw += weight[i];
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }        } /* end of wave */
       }      } /* end of individual */
       /* This for computing forces of mortality (h=1)as a weighted average */    }  else if(mle==2){
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(i=1; i<= nlstate; i++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           gpp[j] += prlim[i][i]*p3mat[i][j][1];        for(mi=1; mi<= wav[i]-1; mi++){
       }              for (ii=1;ii<=nlstate+ndeath;ii++)
       /* end force of mortality */            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1; i<=npar; i++) /* Computes gradient */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for(d=0; d<=dh[mi][i]; d++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if (popbased==1) {            for (kk=1; kk<=cptcovage;kk++) {
         for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           prlim[i][i]=probs[(int)age][i][ij];            }
       }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(j=1; j<= nlstate; j++){            savm=oldm;
         for(h=0; h<=nhstepm; h++){            oldm=newm;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          } /* end mult */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        
         }          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
       /* This for computing force of mortality (h=1)as a weighted average */          bbh=(double)bh[mi][i]/(double)stepm; 
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         for(i=1; i<= nlstate; i++)          ipmx +=1;
           gmp[j] += prlim[i][i]*p3mat[i][j][1];          sw += weight[i];
       }              ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       /* end force of mortality */        } /* end of wave */
       } /* end of individual */
       for(j=1; j<= nlstate; j++) /* vareij */    }  else if(mle==3){  /* exponential inter-extrapolation */
         for(h=0; h<=nhstepm; h++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */          for (ii=1;ii<=nlstate+ndeath;ii++)
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];            for (j=1;j<=nlstate+ndeath;j++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
     } /* End theta */            }
           for(d=0; d<dh[mi][i]; d++){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(h=0; h<=nhstepm; h++) /* veij */            for (kk=1; kk<=cptcovage;kk++) {
       for(j=1; j<=nlstate;j++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(theta=1; theta <=npar; theta++)            }
           trgradg[h][j][theta]=gradg[h][theta][j];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */            savm=oldm;
       for(theta=1; theta <=npar; theta++)            oldm=newm;
         trgradgp[j][theta]=gradgp[theta][j];          } /* end mult */
         
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          s1=s[mw[mi][i]][i];
     for(i=1;i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
       for(j=1;j<=nlstate;j++)          bbh=(double)bh[mi][i]/(double)stepm; 
         vareij[i][j][(int)age] =0.;          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;
     for(h=0;h<=nhstepm;h++){          sw += weight[i];
       for(k=0;k<=nhstepm;k++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        } /* end of wave */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      } /* end of individual */
         for(i=1;i<=nlstate;i++)    }else if (mle==4){  /* ml=4 no inter-extrapolation */
           for(j=1;j<=nlstate;j++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
     /* pptj */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);            }
     for(j=nlstate+1;j<=nlstate+ndeath;j++)          for(d=0; d<dh[mi][i]; d++){
       for(i=nlstate+1;i<=nlstate+ndeath;i++)            newm=savm;
         varppt[j][i]=doldmp[j][i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     /* end ppptj */            for (kk=1; kk<=cptcovage;kk++) {
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);            }
            
     if (popbased==1) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(i=1; i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         prlim[i][i]=probs[(int)age][i][ij];            savm=oldm;
     }            oldm=newm;
              } /* end mult */
     /* This for computing force of mortality (h=1)as a weighted average */        
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){          s1=s[mw[mi][i]][i];
       for(i=1; i<= nlstate; i++)          s2=s[mw[mi+1][i]][i];
         gmp[j] += prlim[i][i]*p3mat[i][j][1];          if( s2 > nlstate){ 
     }                lli=log(out[s1][s2] - savm[s1][s2]);
     /* end force of mortality */          }else{
             lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);          }
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){          ipmx +=1;
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));          sw += weight[i];
       for(i=1; i<=nlstate;i++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][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]); */
       }        } /* end of wave */
     }      } /* end of individual */
     fprintf(ficresprobmorprev,"\n");    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fprintf(ficresvij,"%.0f ",age );        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for(i=1; i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
       for(j=1; j<=nlstate;j++){          for (ii=1;ii<=nlstate+ndeath;ii++)
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);            for (j=1;j<=nlstate+ndeath;j++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficresvij,"\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_matrix(gp,0,nhstepm,1,nlstate);            }
     free_matrix(gm,0,nhstepm,1,nlstate);          for(d=0; d<dh[mi][i]; d++){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            newm=savm;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (kk=1; kk<=cptcovage;kk++) {
   } /* End age */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_vector(gpp,nlstate+1,nlstate+ndeath);            }
   free_vector(gmp,nlstate+1,nlstate+ndeath);          
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");            savm=oldm;
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */            oldm=newm;
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");          } /* end mult */
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);        
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);          s1=s[mw[mi][i]][i];
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);          s2=s[mw[mi+1][i]][i];
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   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);          ipmx +=1;
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   free_vector(xp,1,npar);          /*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]);*/
   free_matrix(doldm,1,nlstate,1,nlstate);        } /* end of wave */
   free_matrix(dnewm,1,nlstate,1,npar);      } /* end of individual */
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    } /* End of if */
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   fclose(ficresprobmorprev);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   fclose(ficgp);    return -l;
   fclose(fichtm);  }
   
 }  /*************** log-likelihood *************/
   double funcone( double *x)
 /************ Variance of prevlim ******************/  {
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    /* Same as likeli but slower because of a lot of printf and if */
 {    int i, ii, j, k, mi, d, kk;
   /* Variance of prevalence limit */    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double **out;
   double **newm;    double lli; /* Individual log likelihood */
   double **dnewm,**doldm;    double llt;
   int i, j, nhstepm, hstepm;    int s1, s2;
   int k, cptcode;    double bbh, survp;
   double *xp;    /*extern weight */
   double *gp, *gm;    /* We are differentiating ll according to initial status */
   double **gradg, **trgradg;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double age,agelim;    /*for(i=1;i<imx;i++) 
   int theta;      printf(" %d\n",s[4][i]);
        */
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    cov[1]=1.;
   fprintf(ficresvpl,"# Age");  
   for(i=1; i<=nlstate;i++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   xp=vector(1,npar);      for(mi=1; mi<= wav[i]-1; mi++){
   dnewm=matrix(1,nlstate,1,npar);        for (ii=1;ii<=nlstate+ndeath;ii++)
   doldm=matrix(1,nlstate,1,nlstate);          for (j=1;j<=nlstate+ndeath;j++){
              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   hstepm=1*YEARM; /* Every year of age */            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          }
   agelim = AGESUP;        for(d=0; d<dh[mi][i]; d++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          newm=savm;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if (stepm >= YEARM) hstepm=1;          for (kk=1; kk<=cptcovage;kk++) {
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     gradg=matrix(1,npar,1,nlstate);          }
     gp=vector(1,nlstate);          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
     gm=vector(1,nlstate);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(theta=1; theta <=npar; theta++){          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
       for(i=1; i<=npar; i++){ /* Computes gradient */          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          savm=oldm;
       }          oldm=newm;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } /* end mult */
       for(i=1;i<=nlstate;i++)        
         gp[i] = prlim[i][i];        s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
       for(i=1; i<=npar; i++) /* Computes gradient */        bbh=(double)bh[mi][i]/(double)stepm; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        /* bias is positive if real duration
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);         * is higher than the multiple of stepm and negative otherwise.
       for(i=1;i<=nlstate;i++)         */
         gm[i] = prlim[i][i];        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
       for(i=1;i<=nlstate;i++)        } else if  (s2==-2) {
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          for (j=1,survp=0. ; j<=nlstate; j++) 
     } /* End theta */            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);
     trgradg =matrix(1,nlstate,1,npar);        }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     for(j=1; j<=nlstate;j++)        } else if(mle==2){
       for(theta=1; theta <=npar; theta++)          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 */
         trgradg[j][theta]=gradg[theta][j];        } 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 */
     for(i=1;i<=nlstate;i++)        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       varpl[i][(int)age] =0.;          lli=log(out[s1][s2]); /* Original formula */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        } else{  /* mle=0 back to 1 */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     for(i=1;i<=nlstate;i++)          /*lli=log(out[s1][s2]); */ /* Original formula */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        } /* End of if */
         ipmx +=1;
     fprintf(ficresvpl,"%.0f ",age );        sw += weight[i];
     for(i=1; i<=nlstate;i++)        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     fprintf(ficresvpl,"\n");        if(globpr){
     free_vector(gp,1,nlstate);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
     free_vector(gm,1,nlstate);   %11.6f %11.6f %11.6f ", \
     free_matrix(gradg,1,npar,1,nlstate);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     free_matrix(trgradg,1,nlstate,1,npar);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   } /* End age */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
   free_vector(xp,1,npar);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   free_matrix(doldm,1,nlstate,1,npar);          }
   free_matrix(dnewm,1,nlstate,1,nlstate);          fprintf(ficresilk," %10.6f\n", -llt);
         }
 }      } /* end of wave */
     } /* end of individual */
 /************ Variance of one-step probabilities  ******************/    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    /* 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 */
   int i, j=0,  i1, k1, l1, t, tj;    if(globpr==0){ /* First time we count the contributions and weights */
   int k2, l2, j1,  z1;      gipmx=ipmx;
   int k=0,l, cptcode;      gsw=sw;
   int first=1, first1;    }
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;    return -l;
   double **dnewm,**doldm;  }
   double *xp;  
   double *gp, *gm;  
   double **gradg, **trgradg;  /*************** function likelione ***********/
   double **mu;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   double age,agelim, cov[NCOVMAX];  {
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */    /* This routine should help understanding what is done with 
   int theta;       the selection of individuals/waves and
   char fileresprob[FILENAMELENGTH];       to check the exact contribution to the likelihood.
   char fileresprobcov[FILENAMELENGTH];       Plotting could be done.
   char fileresprobcor[FILENAMELENGTH];     */
     int k;
   double ***varpij;  
     if(*globpri !=0){ /* Just counts and sums, no printings */
   strcpy(fileresprob,"prob");      strcpy(fileresilk,"ilk"); 
   strcat(fileresprob,fileres);      strcat(fileresilk,fileres);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprob);        printf("Problem with resultfile: %s\n", fileresilk);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   }      }
   strcpy(fileresprobcov,"probcov");      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");
   strcat(fileresprobcov,fileres);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     printf("Problem with resultfile: %s\n", fileresprobcov);      for(k=1; k<=nlstate; k++) 
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   }      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   strcpy(fileresprobcor,"probcor");    }
   strcat(fileresprobcor,fileres);  
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    *fretone=(*funcone)(p);
     printf("Problem with resultfile: %s\n", fileresprobcor);    if(*globpri !=0){
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);      fclose(ficresilk);
   }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);      fflush(fichtm); 
   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);    return;
   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);  
    /*********** Maximum Likelihood Estimation ***************/
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");  
   fprintf(ficresprob,"# Age");  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");  {
   fprintf(ficresprobcov,"# Age");    int i,j, iter=0;
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    double **xi;
   fprintf(ficresprobcov,"# Age");    double fret;
     double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=(nlstate+ndeath);j++){  #ifdef NLOPT
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    int creturn;
       fprintf(ficresprobcov," p%1d-%1d ",i,j);    nlopt_opt opt;
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     }      double *lb;
   fprintf(ficresprob,"\n");    double minf; /* the minimum objective value, upon return */
   fprintf(ficresprobcov,"\n");    double * p1; /* Shifted parameters from 0 instead of 1 */
   fprintf(ficresprobcor,"\n");    myfunc_data dinst, *d = &dinst;
   xp=vector(1,npar);  #endif
   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);    xi=matrix(1,npar,1,npar);
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);    for (i=1;i<=npar;i++)
   first=1;      for (j=1;j<=npar;j++)
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    strcpy(filerespow,"pow"); 
     exit(0);    strcat(filerespow,fileres);
   }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   else{      printf("Problem with resultfile: %s\n", filerespow);
     fprintf(ficgp,"\n# Routine varprob");      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   }    }
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     printf("Problem with html file: %s\n", optionfilehtm);    for (i=1;i<=nlstate;i++)
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);      for(j=1;j<=nlstate+ndeath;j++)
     exit(0);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   }    fprintf(ficrespow,"\n");
   else{  #ifdef POWELL
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");    powell(p,xi,npar,ftol,&iter,&fret,func);
     fprintf(fichtm,"\n");  #endif
   
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");  #ifdef NLOPT
     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");  #ifdef NEWUOA
     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");    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   #else
   }    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   #endif
      lb=vector(0,npar-1);
   cov[1]=1;    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
   tj=cptcoveff;    nlopt_set_lower_bounds(opt, lb);
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}    nlopt_set_initial_step1(opt, 0.1);
   j1=0;    
   for(t=1; t<=tj;t++){    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     for(i1=1; i1<=ncodemax[t];i1++){    d->function = func;
       j1++;    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
          nlopt_set_min_objective(opt, myfunc, d);
       if  (cptcovn>0) {    nlopt_set_xtol_rel(opt, ftol);
         fprintf(ficresprob, "\n#********** Variable ");    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      printf("nlopt failed! %d\n",creturn); 
         fprintf(ficresprob, "**********\n#");    }
         fprintf(ficresprobcov, "\n#********** Variable ");    else {
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
         fprintf(ficresprobcov, "**********\n#");      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
              iter=1; /* not equal */
         fprintf(ficgp, "\n#********** Variable ");    }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    nlopt_destroy(opt);
         fprintf(ficgp, "**********\n#");  #endif
            free_matrix(xi,1,npar,1,npar);
            fclose(ficrespow);
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
          
         fprintf(ficresprobcor, "\n#********** Variable ");      }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficgp, "**********\n#");      /**** Computes Hessian and covariance matrix ***/
       }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
        {
       for (age=bage; age<=fage; age ++){    double  **a,**y,*x,pd;
         cov[2]=age;    double **hess;
         for (k=1; k<=cptcovn;k++) {    int i, j;
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    int *indx;
         }  
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
         for (k=1; k<=cptcovprod;k++)    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    void lubksb(double **a, int npar, int *indx, double b[]) ;
            void ludcmp(double **a, int npar, int *indx, double *d) ;
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));    double gompertz(double p[]);
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    hess=matrix(1,npar,1,npar);
         gp=vector(1,(nlstate)*(nlstate+ndeath));  
         gm=vector(1,(nlstate)*(nlstate+ndeath));    printf("\nCalculation of the hessian matrix. Wait...\n");
        fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         for(theta=1; theta <=npar; theta++){    for (i=1;i<=npar;i++){
           for(i=1; i<=npar; i++)      printf("%d",i);fflush(stdout);
             xp[i] = x[i] + (i==theta ?delti[theta]:0);      fprintf(ficlog,"%d",i);fflush(ficlog);
               
           pmij(pmmij,cov,ncovmodel,xp,nlstate);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
                
           k=0;      /*  printf(" %f ",p[i]);
           for(i=1; i<= (nlstate); i++){          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
             for(j=1; j<=(nlstate+ndeath);j++){    }
               k=k+1;    
               gp[k]=pmmij[i][j];    for (i=1;i<=npar;i++) {
             }      for (j=1;j<=npar;j++)  {
           }        if (j>i) { 
                    printf(".%d%d",i,j);fflush(stdout);
           for(i=1; i<=npar; i++)          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
             xp[i] = x[i] - (i==theta ?delti[theta]:0);          hess[i][j]=hessij(p,delti,i,j,func,npar);
              
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          hess[j][i]=hess[i][j];    
           k=0;          /*printf(" %lf ",hess[i][j]);*/
           for(i=1; i<=(nlstate); i++){        }
             for(j=1; j<=(nlstate+ndeath);j++){      }
               k=k+1;    }
               gm[k]=pmmij[i][j];    printf("\n");
             }    fprintf(ficlog,"\n");
           }  
          printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      
         }    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)    x=vector(1,npar);
           for(theta=1; theta <=npar; theta++)    indx=ivector(1,npar);
             trgradg[j][theta]=gradg[theta][j];    for (i=1;i<=npar;i++)
              for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);    ludcmp(a,npar,indx,&pd);
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);  
            for (j=1;j<=npar;j++) {
         pmij(pmmij,cov,ncovmodel,x,nlstate);      for (i=1;i<=npar;i++) x[i]=0;
              x[j]=1;
         k=0;      lubksb(a,npar,indx,x);
         for(i=1; i<=(nlstate); i++){      for (i=1;i<=npar;i++){ 
           for(j=1; j<=(nlstate+ndeath);j++){        matcov[i][j]=x[i];
             k=k+1;      }
             mu[k][(int) age]=pmmij[i][j];    }
           }  
         }    printf("\n#Hessian matrix#\n");
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)    fprintf(ficlog,"\n#Hessian matrix#\n");
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)    for (i=1;i<=npar;i++) { 
             varpij[i][j][(int)age] = doldm[i][j];      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
         /*printf("\n%d ",(int)age);        fprintf(ficlog,"%.3e ",hess[i][j]);
      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]));      printf("\n");
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      fprintf(ficlog,"\n");
      }*/    }
   
         fprintf(ficresprob,"\n%d ",(int)age);    /* Recompute Inverse */
         fprintf(ficresprobcov,"\n%d ",(int)age);    for (i=1;i<=npar;i++)
         fprintf(ficresprobcor,"\n%d ",(int)age);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)  
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));    /*  printf("\n#Hessian matrix recomputed#\n");
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);    for (j=1;j<=npar;j++) {
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);      for (i=1;i<=npar;i++) x[i]=0;
         }      x[j]=1;
         i=0;      lubksb(a,npar,indx,x);
         for (k=1; k<=(nlstate);k++){      for (i=1;i<=npar;i++){ 
           for (l=1; l<=(nlstate+ndeath);l++){        y[i][j]=x[i];
             i=i++;        printf("%.3e ",y[i][j]);
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);        fprintf(ficlog,"%.3e ",y[i][j]);
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);      }
             for (j=1; j<=i;j++){      printf("\n");
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);      fprintf(ficlog,"\n");
               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 */    free_matrix(a,1,npar,1,npar);
       } /* end of loop for age */    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
       /* Confidence intervalle of pij  */    free_ivector(indx,1,npar);
       /*    free_matrix(hess,1,npar,1,npar);
       fprintf(ficgp,"\nset noparametric;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);  /*************** hessian matrix ****************/
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);  {
       */    int i;
     int l=1, lmax=20;
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/    double k1,k2;
       first1=1;    double p2[MAXPARM+1]; /* identical to x */
       for (k1=1; k1<=(nlstate);k1++){    double res;
         for (l1=1; l1<=(nlstate+ndeath);l1++){    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           if(l1==k1) continue;    double fx;
           i=(k1-1)*(nlstate+ndeath)+l1;    int k=0,kmax=10;
           for (k2=1; k2<=(nlstate);k2++){    double l1;
             for (l2=1; l2<=(nlstate+ndeath);l2++){  
               if(l2==k2) continue;    fx=func(x);
               j=(k2-1)*(nlstate+ndeath)+l2;    for (i=1;i<=npar;i++) p2[i]=x[i];
               if(j<=i) continue;    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
               for (age=bage; age<=fage; age ++){      l1=pow(10,l);
                 if ((int)age %5==0){      delts=delt;
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;      for(k=1 ; k <kmax; k=k+1){
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;        delt = delta*(l1*k);
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;        p2[theta]=x[theta] +delt;
                   mu1=mu[i][(int) age]/stepm*YEARM ;        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
                   mu2=mu[j][(int) age]/stepm*YEARM;        p2[theta]=x[theta]-delt;
                   /* Computing eigen value of matrix of covariance */        k2=func(p2)-fx;
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));        /*res= (k1-2.0*fx+k2)/delt/delt; */
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
                   if(first1==1){        
                     first1=0;  #ifdef DEBUGHESS
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
                   }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
                   fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);  #endif
                   /* Eigen vectors */        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
                   v21=sqrt(1.-v11*v11);          k=kmax;
                   v12=-v21;        }
                   v22=v11;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
                   /*printf(fignu*/          k=kmax; l=lmax*10;
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */        }
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
                   if(first==1){          delts=delt;
                     first=0;        }
                     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);    }
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    delti[theta]=delts;
                     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);    return res; 
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);    
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);  }
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);  
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
                     /*              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), \    int i;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    int l=1, lmax=20;
                     */    double k1,k2,k3,k4,res,fx;
                     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",\    double p2[MAXPARM+1];
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    int k;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));  
                   }else{    fx=func(x);
                     first=0;    for (k=1; k<=2; k++) {
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);      for (i=1;i<=npar;i++) p2[i]=x[i];
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);      p2[thetai]=x[thetai]+delti[thetai]/k;
                     /*      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                     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\"",\      k1=func(p2)-fx;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);      p2[thetai]=x[thetai]+delti[thetai]/k;
                     */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                     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",\      k2=func(p2)-fx;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));      p2[thetai]=x[thetai]-delti[thetai]/k;
                   }/* if first */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                 } /* age mod 5 */      k3=func(p2)-fx;
               } /* end loop age */    
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);      p2[thetai]=x[thetai]-delti[thetai]/k;
               first=1;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
             } /*l12 */      k4=func(p2)-fx;
           } /* k12 */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         } /*l1 */  #ifdef DEBUG
       }/* k1 */      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);
     } /* loop covariates */      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);
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);  #endif
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    return res;
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);  }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  /************** Inverse of matrix **************/
   }  void ludcmp(double **a, int n, int *indx, double *d) 
   free_vector(xp,1,npar);  { 
   fclose(ficresprob);    int i,imax,j,k; 
   fclose(ficresprobcov);    double big,dum,sum,temp; 
   fclose(ficresprobcor);    double *vv; 
   fclose(ficgp);   
   fclose(fichtm);    vv=vector(1,n); 
 }    *d=1.0; 
     for (i=1;i<=n;i++) { 
       big=0.0; 
 /******************* Printing html file ***********/      for (j=1;j<=n;j++) 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \        if ((temp=fabs(a[i][j])) > big) big=temp; 
                   int lastpass, int stepm, int weightopt, char model[],\      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\      vv[i]=1.0/big; 
                   int popforecast, int estepm ,\    } 
                   double jprev1, double mprev1,double anprev1, \    for (j=1;j<=n;j++) { 
                   double jprev2, double mprev2,double anprev2){      for (i=1;i<j;i++) { 
   int jj1, k1, i1, cpt;        sum=a[i][j]; 
   /*char optionfilehtm[FILENAMELENGTH];*/        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {        a[i][j]=sum; 
     printf("Problem with %s \n",optionfilehtm), exit(0);      } 
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);      big=0.0; 
   }      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n        for (k=1;k<j;k++) 
  - 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          sum -= a[i][k]*a[k][j]; 
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n        a[i][j]=sum; 
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n        if ( (dum=vv[i]*fabs(sum)) >= big) { 
  - Life expectancies by age and initial health status (estepm=%2d months):          big=dum; 
    <a href=\"e%s\">e%s</a> <br>\n</li>", \          imax=i; 
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);        } 
       } 
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");      if (j != imax) { 
         for (k=1;k<=n;k++) { 
  m=cptcoveff;          dum=a[imax][k]; 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
  jj1=0;        } 
  for(k1=1; k1<=m;k1++){        *d = -(*d); 
    for(i1=1; i1<=ncodemax[k1];i1++){        vv[imax]=vv[j]; 
      jj1++;      } 
      if (cptcovn > 0) {      indx[j]=imax; 
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      if (a[j][j] == 0.0) a[j][j]=TINY; 
        for (cpt=1; cpt<=cptcoveff;cpt++)      if (j != n) { 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        dum=1.0/(a[j][j]); 
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
      }      } 
      /* Pij */    } 
      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>    free_vector(vv,1,n);  /* Doesn't work */
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),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: pe%s%d2.png<br>  
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  void lubksb(double **a, int n, int *indx, double b[]) 
        /* Stable prevalence in each health state */  { 
        for(cpt=1; cpt<nlstate;cpt++){    int i,ii=0,ip,j; 
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    double sum; 
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);   
        }    for (i=1;i<=n;i++) { 
      for(cpt=1; cpt<=nlstate;cpt++) {      ip=indx[i]; 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>      sum=b[ip]; 
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      b[ip]=b[i]; 
      }      if (ii) 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
 health expectancies in states (1) and (2): e%s%d.png<br>      else if (sum) ii=i; 
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      b[i]=sum; 
    } /* end i1 */    } 
  }/* End k1 */    for (i=n;i>=1;i--) { 
  fprintf(fichtm,"</ul>");      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n    } 
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n  } 
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n  
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n  void pstamp(FILE *fichier)
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n  {
  - 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(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
  - 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);  
   /************ Frequencies ********************/
  if(popforecast==1) fprintf(fichtm,"\n  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[])
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n  {  /* Some frequencies */
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    
         <br>",fileres,fileres,fileres,fileres);    int i, m, jk, j1, bool, z1,j;
  else    int first;
    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);    double ***freq; /* Frequencies */
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");    double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
  m=cptcoveff;    char fileresp[FILENAMELENGTH];
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    
     pp=vector(1,nlstate);
  jj1=0;    prop=matrix(1,nlstate,iagemin,iagemax+3);
  for(k1=1; k1<=m;k1++){    strcpy(fileresp,"p");
    for(i1=1; i1<=ncodemax[k1];i1++){    strcat(fileresp,fileres);
      jj1++;    if((ficresp=fopen(fileresp,"w"))==NULL) {
      if (cptcovn > 0) {      printf("Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
        for (cpt=1; cpt<=cptcoveff;cpt++)      exit(0);
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
      }    j1=0;
      for(cpt=1; cpt<=nlstate;cpt++) {    
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    j=cptcoveff;
 interval) in state (%d): v%s%d%d.png <br>    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
      }    first=1;
    } /* end i1 */  
  }/* End k1 */    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
  fprintf(fichtm,"</ul>");    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
 fclose(fichtm);    /*    j1++; */
 }    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 /******************* Gnuplot file **************/          scanf("%d", i);*/
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        for (i=-5; i<=nlstate+ndeath; i++)  
           for (jk=-5; jk<=nlstate+ndeath; jk++)  
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;            for(m=iagemin; m <= iagemax+3; m++)
   int ng;              freq[i][jk][m]=0;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        
     printf("Problem with file %s",optionfilegnuplot);        for (i=1; i<=nlstate; i++)  
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);          for(m=iagemin; m <= iagemax+3; m++)
   }            prop[i][m]=0;
         
 #ifdef windows        dateintsum=0;
     fprintf(ficgp,"cd \"%s\" \n",pathc);        k2cpt=0;
 #endif        for (i=1; i<=imx; i++) {
 m=pow(2,cptcoveff);          bool=1;
            if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
  /* 1eme*/            for (z1=1; z1<=cptcoveff; z1++)       
   for (cpt=1; cpt<= nlstate ; cpt ++) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
    for (k1=1; k1<= m ; k1 ++) {                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
                 bool=0;
 #ifdef windows                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
      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);                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
 #endif                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
 #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);   
 #endif          if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
 for (i=1; i<= nlstate ; i ++) {              k2=anint[m][i]+(mint[m][i]/12.);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     for (i=1; i<= nlstate ; i ++) {                if (m<lastpass) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
 }                }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);                
      for (i=1; i<= nlstate ; i ++) {                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                  dateintsum=dateintsum+k2;
   else fprintf(ficgp," \%%*lf (\%%*lf)");                  k2cpt++;
 }                  }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                /*}*/
 #ifdef unix            }
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");          }
 #endif        } /* end i */
    }         
   }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   /*2 eme*/        pstamp(ficresp);
         if  (cptcovn>0) {
   for (k1=1; k1<= m ; k1 ++) {          fprintf(ficresp, "\n#********** Variable "); 
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);          fprintf(ficresp, "**********\n#");
              fprintf(ficlog, "\n#********** Variable "); 
     for (i=1; i<= nlstate+1 ; i ++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       k=2*i;          fprintf(ficlog, "**********\n#");
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        }
       for (j=1; j<= nlstate+1 ; j ++) {        for(i=1; i<=nlstate;i++) 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   else fprintf(ficgp," \%%*lf (\%%*lf)");        fprintf(ficresp, "\n");
 }          
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        for(i=iagemin; i <= iagemax+3; i++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          if(i==iagemax+3){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            fprintf(ficlog,"Total");
       for (j=1; j<= nlstate+1 ; j ++) {          }else{
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            if(first==1){
         else fprintf(ficgp," \%%*lf (\%%*lf)");              first=0;
 }                printf("See log file for details...\n");
       fprintf(ficgp,"\" t\"\" w l 0,");            }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);            fprintf(ficlog,"Age %d", i);
       for (j=1; j<= nlstate+1 ; j ++) {          }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for(jk=1; jk <=nlstate ; jk++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 }                pp[jk] += freq[jk][m][i]; 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          }
       else fprintf(ficgp,"\" t\"\" w l 0,");          for(jk=1; jk <=nlstate ; jk++){
     }            for(m=-1, pos=0; m <=0 ; m++)
   }              pos += freq[jk][m][i];
              if(pp[jk]>=1.e-10){
   /*3eme*/              if(first==1){
                 printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   for (k1=1; k1<= m ; k1 ++) {              }
     for (cpt=1; cpt<= nlstate ; cpt ++) {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       k=2+nlstate*(2*cpt-2);            }else{
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);              if(first==1)
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            }
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          }
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          for(jk=1; jk <=nlstate ; jk++){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
 */          }       
       for (i=1; i< nlstate ; i ++) {          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         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);            pos += pp[jk];
             posprop += prop[jk][i];
       }          }
     }          for(jk=1; jk <=nlstate ; jk++){
   }            if(pos>=1.e-5){
                if(first==1)
   /* CV preval stat */                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for (k1=1; k1<= m ; k1 ++) {              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for (cpt=1; cpt<nlstate ; cpt ++) {            }else{
       k=3;              if(first==1)
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
       for (i=1; i< nlstate ; i ++)            if( i <= iagemax){
         fprintf(ficgp,"+$%d",k+i+1);              if(pos>=1.e-5){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                      /*probs[i][jk][j1]= pp[jk]/pos;*/
       l=3+(nlstate+ndeath)*cpt;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);              }
       for (i=1; i< nlstate ; i ++) {              else
         l=3+(nlstate+ndeath)*cpt;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
         fprintf(ficgp,"+$%d",l+i+1);            }
       }          }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            
     }          for(jk=-1; jk <=nlstate+ndeath; jk++)
   }              for(m=-1; m <=nlstate+ndeath; m++)
                if(freq[jk][m][i] !=0 ) {
   /* proba elementaires */              if(first==1)
    for(i=1,jk=1; i <=nlstate; i++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(k=1; k <=(nlstate+ndeath); k++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       if (k != i) {              }
         for(j=1; j <=ncovmodel; j++){          if(i <= iagemax)
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            fprintf(ficresp,"\n");
           jk++;          if(first==1)
           fprintf(ficgp,"\n");            printf("Others in log...\n");
         }          fprintf(ficlog,"\n");
       }        }
     }        /*}*/
    }    }
     dateintmean=dateintsum/k2cpt; 
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/   
      for(jk=1; jk <=m; jk++) {    fclose(ficresp);
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
        if (ng==2)    free_vector(pp,1,nlstate);
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
        else    /* End of Freq */
          fprintf(ficgp,"\nset title \"Probability\"\n");  }
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);  
        i=1;  /************ Prevalence ********************/
        for(k2=1; k2<=nlstate; k2++) {  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)
          k3=i;  {  
          for(k=1; k<=(nlstate+ndeath); k++) {    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
            if (k != k2){       in each health status at the date of interview (if between dateprev1 and dateprev2).
              if(ng==2)       We still use firstpass and lastpass as another selection.
                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);    int i, m, jk, j1, bool, z1,j;
              ij=1;  
              for(j=3; j <=ncovmodel; j++) {    double **prop;
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double posprop; 
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double  y2; /* in fractional years */
                  ij++;    int iagemin, iagemax;
                }    int first; /** to stop verbosity which is redirected to log file */
                else  
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    iagemin= (int) agemin;
              }    iagemax= (int) agemax;
              fprintf(ficgp,")/(1");    /*pp=vector(1,nlstate);*/
                  prop=matrix(1,nlstate,iagemin,iagemax+3); 
              for(k1=1; k1 <=nlstate; k1++){      /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    j1=0;
                ij=1;    
                for(j=3; j <=ncovmodel; j++){    /*j=cptcoveff;*/
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    
                    ij++;    first=1;
                  }    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
                  else      /*for(i1=1; i1<=ncodemax[k1];i1++){
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        j1++;*/
                }        
                fprintf(ficgp,")");        for (i=1; i<=nlstate; i++)  
              }          for(m=iagemin; m <= iagemax+3; m++)
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);            prop[i][m]=0.0;
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");       
              i=i+ncovmodel;        for (i=1; i<=imx; i++) { /* Each individual */
            }          bool=1;
          } /* end k */          if  (cptcovn>0) {
        } /* end k2 */            for (z1=1; z1<=cptcoveff; z1++) 
      } /* end jk */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
    } /* end ng */                bool=0;
    fclose(ficgp);          } 
 }  /* end gnuplot */          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
 /*************** Moving average **************/              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
   int i, cpt, cptcod;                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); 
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)                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]]);*/
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
           mobaverage[(int)agedeb][i][cptcod]=0.;                  prop[s[m][i]][iagemax+3] += weight[i]; 
                    } 
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){              }
       for (i=1; i<=nlstate;i++){            } /* end selection of waves */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          }
           for (cpt=0;cpt<=4;cpt++){        }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        for(i=iagemin; i <= iagemax+3; i++){  
           }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;            posprop += prop[jk][i]; 
         }          } 
       }          
     }          for(jk=1; jk <=nlstate ; jk++){     
                if( i <=  iagemax){ 
 }              if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
               } else{
 /************** Forecasting ******************/                if(first==1){
 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){                  first=0;
                    printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                }
   int *popage;              }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            } 
   double *popeffectif,*popcount;          }/* end jk */ 
   double ***p3mat;        }/* end i */ 
   char fileresf[FILENAMELENGTH];      /*} *//* end i1 */
     } /* end j1 */
  agelim=AGESUP;    
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     /*free_vector(pp,1,nlstate);*/
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
    }  /* End of prevalence */
    
   strcpy(fileresf,"f");  /************* Waves Concatenation ***************/
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {  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)
     printf("Problem with forecast resultfile: %s\n", fileresf);  {
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   }       Death is a valid wave (if date is known).
   printf("Computing forecasting: result on file '%s' \n", fileresf);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
   if (cptcoveff==0) ncodemax[cptcoveff]=1;       */
   
   if (mobilav==1) {    int i, mi, m;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     movingaverage(agedeb, fage, ageminpar, mobaverage);       double sum=0., jmean=0.;*/
   }    int first;
     int j, k=0,jk, ju, jl;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double sum=0.;
   if (stepm<=12) stepsize=1;    first=0;
      jmin=100000;
   agelim=AGESUP;    jmax=-1;
      jmean=0.;
   hstepm=1;    for(i=1; i<=imx; i++){
   hstepm=hstepm/stepm;      mi=0;
   yp1=modf(dateintmean,&yp);      m=firstpass;
   anprojmean=yp;      while(s[m][i] <= nlstate){
   yp2=modf((yp1*12),&yp);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   mprojmean=yp;          mw[++mi][i]=m;
   yp1=modf((yp2*30.5),&yp);        if(m >=lastpass)
   jprojmean=yp;          break;
   if(jprojmean==0) jprojmean=1;        else
   if(mprojmean==0) jprojmean=1;          m++;
        }/* end while */
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      if (s[m][i] > nlstate){
          mi++;     /* Death is another wave */
   for(cptcov=1;cptcov<=i2;cptcov++){        /* if(mi==0)  never been interviewed correctly before death */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){           /* Only death is a correct wave */
       k=k+1;        mw[mi][i]=m;
       fprintf(ficresf,"\n#******");      }
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      wav[i]=mi;
       }      if(mi==0){
       fprintf(ficresf,"******\n");        nbwarn++;
       fprintf(ficresf,"# StartingAge FinalAge");        if(first==0){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
                first=1;
              }
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        if(first==1){
         fprintf(ficresf,"\n");          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          }
       } /* end mi==0 */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    } /* End individuals */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;    for(i=1; i<=imx; i++){
                for(mi=1; mi<wav[i];mi++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if (stepm <=0)
           oldm=oldms;savm=savms;          dh[mi][i]=1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          else{
                  if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           for (h=0; h<=nhstepm; h++){            if (agedc[i] < 2*AGESUP) {
             if (h==(int) (calagedate+YEARM*cpt)) {              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);              if(j==0) j=1;  /* Survives at least one month after exam */
             }              else if(j<0){
             for(j=1; j<=nlstate+ndeath;j++) {                nberr++;
               kk1=0.;kk2=0;                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]);
               for(i=1; i<=nlstate;i++) {                              j=1; /* Temporary Dangerous patch */
                 if (mobilav==1)                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);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                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]);
                 else {                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);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              }
                 }              k=k+1;
                              if (j >= jmax){
               }                jmax=j;
               if (h==(int)(calagedate+12*cpt)){                ijmax=i;
                 fprintf(ficresf," %.3f", kk1);              }
                                      if (j <= jmin){
               }                jmin=j;
             }                ijmin=i;
           }              }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              sum=sum+j;
         }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     }            }
   }          }
                  else{
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            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]); */
   fclose(ficresf);  
 }            k=k+1;
 /************** Forecasting ******************/            if (j >= jmax) {
 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){              jmax=j;
                ijmax=i;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            }
   int *popage;            else if (j <= jmin){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              jmin=j;
   double *popeffectif,*popcount;              ijmin=i;
   double ***p3mat,***tabpop,***tabpopprev;            }
   char filerespop[FILENAMELENGTH];            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            if(j<0){
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              nberr++;
   agelim=AGESUP;              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]);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;              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]);
              }
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            sum=sum+j;
            }
            jk= j/stepm;
   strcpy(filerespop,"pop");          jl= j -jk*stepm;
   strcat(filerespop,fileres);          ju= j -(jk+1)*stepm;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     printf("Problem with forecast resultfile: %s\n", filerespop);            if(jl==0){
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);              dh[mi][i]=jk;
   }              bh[mi][i]=0;
   printf("Computing forecasting: result on file '%s' \n", filerespop);            }else{ /* We want a negative bias in order to only have interpolation ie
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);                    * to avoid the price of an extra matrix product in likelihood */
               dh[mi][i]=jk+1;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;              bh[mi][i]=ju;
             }
   if (mobilav==1) {          }else{
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            if(jl <= -ju){
     movingaverage(agedeb, fage, ageminpar, mobaverage);              dh[mi][i]=jk;
   }              bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
   stepsize=(int) (stepm+YEARM-1)/YEARM;                                   */
   if (stepm<=12) stepsize=1;            }
              else{
   agelim=AGESUP;              dh[mi][i]=jk+1;
                bh[mi][i]=ju;
   hstepm=1;            }
   hstepm=hstepm/stepm;            if(dh[mi][i]==0){
                dh[mi][i]=1; /* At least one step */
   if (popforecast==1) {              bh[mi][i]=ju; /* At least one step */
     if((ficpop=fopen(popfile,"r"))==NULL) {              /*  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("Problem with population file : %s\n",popfile);exit(0);            }
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);          } /* end if mle */
     }        }
     popage=ivector(0,AGESUP);      } /* end wave */
     popeffectif=vector(0,AGESUP);    }
     popcount=vector(0,AGESUP);    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);
     i=1;      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);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;   }
      
     imx=i;  /*********** Tricode ****************************/
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   }  {
     /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   for(cptcov=1;cptcov<=i2;cptcov++){    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){     * Boring subroutine which should only output nbcode[Tvar[j]][k]
       k=k+1;     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
       fprintf(ficrespop,"\n#******");     * nbcode[Tvar[j]][1]= 
       for(j=1;j<=cptcoveff;j++) {    */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
       fprintf(ficrespop,"******\n");    int modmaxcovj=0; /* Modality max of covariates j */
       fprintf(ficrespop,"# Age");    int cptcode=0; /* Modality max of covariates j */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    int modmincovj=0; /* Modality min of covariates j */
       if (popforecast==1)  fprintf(ficrespop," [Population]");  
        
       for (cpt=0; cpt<=0;cpt++) {    cptcoveff=0; 
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);     
            for (k=-1; k < maxncov; k++) Ndum[k]=0;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;    /* Loop on covariates without age and products */
              for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
           oldm=oldms;savm=savms;                                 modality of this covariate Vj*/ 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          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 *:
           for (h=0; h<=nhstepm; h++){                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
             if (h==(int) (calagedate+YEARM*cpt)) {                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
             }                                        modality of the nth covariate of individual i. */
             for(j=1; j<=nlstate+ndeath;j++) {        if (ij > modmaxcovj)
               kk1=0.;kk2=0;          modmaxcovj=ij; 
               for(i=1; i<=nlstate;i++) {                      else if (ij < modmincovj) 
                 if (mobilav==1)          modmincovj=ij; 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        if ((ij < -1) && (ij > NCOVMAX)){
                 else {          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          exit(1);
                 }        }else
               }        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
               if (h==(int)(calagedate+12*cpt)){        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                   /*fprintf(ficrespop," %.3f", kk1);        /* getting the maximum value of the modality of the covariate
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
               }           female is 1, then modmaxcovj=1.*/
             }      }
             for(i=1; i<=nlstate;i++){      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
               kk1=0.;      cptcode=modmaxcovj;
                 for(j=1; j<=nlstate;j++){      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];     /*for (i=0; i<=cptcode; i++) {*/
                 }      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
             }        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
           ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        }
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        /* 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 */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } /* Ndum[-1] number of undefined modalities */
         }  
       }      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
        /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
   /******/      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
          modmincovj=3; modmaxcovj = 7;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);           which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){         variables V1_1 and V1_2.
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);         nbcode[Tvar[j]][ij]=k;
           nhstepm = nhstepm/hstepm;         nbcode[Tvar[j]][1]=0;
                   nbcode[Tvar[j]][2]=1;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         nbcode[Tvar[j]][3]=2;
           oldm=oldms;savm=savms;      */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        ij=1; /* ij is similar to i but can jumps over null modalities */
           for (h=0; h<=nhstepm; h++){      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
             if (h==(int) (calagedate+YEARM*cpt)) {        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          /*recode from 0 */
             }          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
             for(j=1; j<=nlstate+ndeath;j++) {            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
               kk1=0.;kk2=0;                                       k is a modality. If we have model=V1+V1*sex 
               for(i=1; i<=nlstate;i++) {                                                     then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                ij++;
               }          }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);          if (ij > ncodemax[j]) break; 
             }        }  /* end of loop on */
           }      } /* end of loop on modality */ 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
         }    
       }   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
    }    
   }    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
       /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
      Ndum[ij]++; 
   if (popforecast==1) {   } 
     free_ivector(popage,0,AGESUP);  
     free_vector(popeffectif,0,AGESUP);   ij=1;
     free_vector(popcount,0,AGESUP);   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   }     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     if((Ndum[i]!=0) && (i<=ncovcol)){
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
   fclose(ficrespop);       Tvaraff[ij]=i; /*For printing (unclear) */
 }       ij++;
      }else
 /***********************************************/         Tvaraff[ij]=0;
 /**************** Main Program *****************/   }
 /***********************************************/   ij--;
    cptcoveff=ij; /*Number of total covariates*/
 int main(int argc, char *argv[])  
 {  }
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  
   double agedeb, agefin,hf;  /*********** Health Expectancies ****************/
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  
   void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   double fret;  
   double **xi,tmp,delta;  {
     /* Health expectancies, no variances */
   double dum; /* Dummy variable */    int i, j, nhstepm, hstepm, h, nstepm;
   double ***p3mat;    int nhstepma, nstepma; /* Decreasing with age */
   int *indx;    double age, agelim, hf;
   char line[MAXLINE], linepar[MAXLINE];    double ***p3mat;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];    double eip;
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */    pstamp(ficreseij);
   int c,  h , cpt,l;    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   int ju,jl, mi;    fprintf(ficreseij,"# Age");
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    for(i=1; i<=nlstate;i++){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      for(j=1; j<=nlstate;j++){
   int mobilav=0,popforecast=0;        fprintf(ficreseij," e%1d%1d ",i,j);
   int hstepm, nhstepm;      }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;      fprintf(ficreseij," e%1d. ",i);
     }
   double bage, fage, age, agelim, agebase;    fprintf(ficreseij,"\n");
   double ftolpl=FTOL;  
   double **prlim;    
   double *severity;    if(estepm < stepm){
   double ***param; /* Matrix of parameters */      printf ("Problem %d lower than %d\n",estepm, stepm);
   double  *p;    }
   double **matcov; /* Matrix of covariance */    else  hstepm=estepm;   
   double ***delti3; /* Scale */    /* We compute the life expectancy from trapezoids spaced every estepm months
   double *delti; /* Scale */     * This is mainly to measure the difference between two models: for example
   double ***eij, ***vareij;     * if stepm=24 months pijx are given only every 2 years and by summing them
   double **varpl; /* Variances of prevalence limits by age */     * we are calculating an estimate of the Life Expectancy assuming a linear 
   double *epj, vepp;     * progression in between and thus overestimating or underestimating according
   double kk1, kk2;     * to the curvature of the survival function. If, for the same date, we 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
   char *alph[]={"a","a","b","c","d","e"}, str[4];     * curvature will be obtained if estepm is as small as stepm. */
   
     /* For example we decided to compute the life expectancy with the smallest unit */
   char z[1]="c", occ;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 #include <sys/time.h>       nhstepm is the number of hstepm from age to agelim 
 #include <time.h>       nstepm is the number of stepm from age to agelin. 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];       Look at hpijx to understand the reason of that which relies in memory size
         and note for a fixed period like estepm months */
   /* long total_usecs;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   struct timeval start_time, end_time;       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
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   getcwd(pathcd, size);       results. So we changed our mind and took the option of the best precision.
     */
   printf("\n%s",version);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");    agelim=AGESUP;
     scanf("%s",pathtot);    /* If stepm=6 months */
   }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   else{         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     strcpy(pathtot,argv[1]);      
   }  /* nhstepm age range expressed in number of stepm */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   /*cygwin_split_path(pathtot,path,optionfile);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    /* if (stepm >= YEARM) hstepm=1;*/
   /* cutv(path,optionfile,pathtot,'\\');*/    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    for (age=bage; age<=fage; age ++){ 
   chdir(path);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   replace(pathc,path);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
 /*-------- arguments in the command line --------*/      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
   /* Log file */      /* If stepm=6 months */
   strcat(filelog, optionfilefiname);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   strcat(filelog,".log");    /* */         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   if((ficlog=fopen(filelog,"w"))==NULL)    {      
     printf("Problem with logfile %s\n",filelog);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     goto end;      
   }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   fprintf(ficlog,"Log filename:%s\n",filelog);      
   fprintf(ficlog,"\n%s",version);      printf("%d|",(int)age);fflush(stdout);
   fprintf(ficlog,"\nEnter the parameter file name: ");      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      
   fflush(ficlog);      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
   /* */        for(j=1; j<=nlstate;j++)
   strcpy(fileres,"r");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   strcat(fileres, optionfilefiname);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   strcat(fileres,".txt");    /* Other files have txt extension */            
             /* 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]);*/
   /*---------arguments file --------*/  
           }
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  
     printf("Problem with optionfile %s\n",optionfile);      fprintf(ficreseij,"%3.0f",age );
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);      for(i=1; i<=nlstate;i++){
     goto end;        eip=0;
   }        for(j=1; j<=nlstate;j++){
           eip +=eij[i][j][(int)age];
   strcpy(filereso,"o");          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   strcat(filereso,fileres);        }
   if((ficparo=fopen(filereso,"w"))==NULL) {        fprintf(ficreseij,"%9.4f", eip );
     printf("Problem with Output resultfile: %s\n", filereso);      }
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);      fprintf(ficreseij,"\n");
     goto end;      
   }    }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /* Reads comments: lines beginning with '#' */    printf("\n");
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficlog,"\n");
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);  }
     puts(line);  
     fputs(line,ficparo);  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[] )
   }  
   ungetc(c,ficpar);  {
     /* Covariances of health expectancies eij and of total life expectancies according
   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);     to initial status i, ei. .
   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);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
 while((c=getc(ficpar))=='#' && c!= EOF){    int nhstepma, nstepma; /* Decreasing with age */
     ungetc(c,ficpar);    double age, agelim, hf;
     fgets(line, MAXLINE, ficpar);    double ***p3matp, ***p3matm, ***varhe;
     puts(line);    double **dnewm,**doldm;
     fputs(line,ficparo);    double *xp, *xm;
   }    double **gp, **gm;
   ungetc(c,ficpar);    double ***gradg, ***trgradg;
      int theta;
      
   covar=matrix(0,NCOVMAX,1,n);    double eip, vip;
   cptcovn=0;  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     xp=vector(1,npar);
   ncovmodel=2+cptcovn;    xm=vector(1,npar);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    dnewm=matrix(1,nlstate*nlstate,1,npar);
      doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   /* Read guess parameters */    
   /* Reads comments: lines beginning with '#' */    pstamp(ficresstdeij);
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     ungetc(c,ficpar);    fprintf(ficresstdeij,"# Age");
     fgets(line, MAXLINE, ficpar);    for(i=1; i<=nlstate;i++){
     puts(line);      for(j=1; j<=nlstate;j++)
     fputs(line,ficparo);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   }      fprintf(ficresstdeij," e%1d. ",i);
   ungetc(c,ficpar);    }
      fprintf(ficresstdeij,"\n");
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)    pstamp(ficrescveij);
     for(j=1; j <=nlstate+ndeath-1; j++){    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
       fscanf(ficpar,"%1d%1d",&i1,&j1);    fprintf(ficrescveij,"# Age");
       fprintf(ficparo,"%1d%1d",i1,j1);    for(i=1; i<=nlstate;i++)
       if(mle==1)      for(j=1; j<=nlstate;j++){
         printf("%1d%1d",i,j);        cptj= (j-1)*nlstate+i;
       fprintf(ficlog,"%1d%1d",i,j);        for(i2=1; i2<=nlstate;i2++)
       for(k=1; k<=ncovmodel;k++){          for(j2=1; j2<=nlstate;j2++){
         fscanf(ficpar," %lf",&param[i][j][k]);            cptj2= (j2-1)*nlstate+i2;
         if(mle==1){            if(cptj2 <= cptj)
           printf(" %lf",param[i][j][k]);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           fprintf(ficlog," %lf",param[i][j][k]);          }
         }      }
         else    fprintf(ficrescveij,"\n");
           fprintf(ficlog," %lf",param[i][j][k]);    
         fprintf(ficparo," %lf",param[i][j][k]);    if(estepm < stepm){
       }      printf ("Problem %d lower than %d\n",estepm, stepm);
       fscanf(ficpar,"\n");    }
       if(mle==1)    else  hstepm=estepm;   
         printf("\n");    /* We compute the life expectancy from trapezoids spaced every estepm months
       fprintf(ficlog,"\n");     * This is mainly to measure the difference between two models: for example
       fprintf(ficparo,"\n");     * 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
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;     * 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
   p=param[1][1];     * to compare the new estimate of Life expectancy with the same linear 
       * hypothesis. A more precise result, taking into account a more precise
   /* Reads comments: lines beginning with '#' */     * curvature will be obtained if estepm is as small as stepm. */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    /* For example we decided to compute the life expectancy with the smallest unit */
     fgets(line, MAXLINE, ficpar);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     puts(line);       nhstepm is the number of hstepm from age to agelim 
     fputs(line,ficparo);       nstepm is the number of stepm from age to agelin. 
   }       Look at hpijx to understand the reason of that which relies in memory size
   ungetc(c,ficpar);       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       survival function given by stepm (the optimization length). Unfortunately it
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */       means that if the survival funtion is printed only each two years of age and if
   for(i=1; i <=nlstate; i++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     for(j=1; j <=nlstate+ndeath-1; j++){       results. So we changed our mind and took the option of the best precision.
       fscanf(ficpar,"%1d%1d",&i1,&j1);    */
       printf("%1d%1d",i,j);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){    /* If stepm=6 months */
         fscanf(ficpar,"%le",&delti3[i][j][k]);    /* nhstepm age range expressed in number of stepm */
         printf(" %le",delti3[i][j][k]);    agelim=AGESUP;
         fprintf(ficparo," %le",delti3[i][j][k]);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
       }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       fscanf(ficpar,"\n");    /* if (stepm >= YEARM) hstepm=1;*/
       printf("\n");    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       fprintf(ficparo,"\n");    
     }    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   delti=delti3[1][1];    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
      trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   /* Reads comments: lines beginning with '#' */    gp=matrix(0,nhstepm,1,nlstate*nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){    gm=matrix(0,nhstepm,1,nlstate*nlstate);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    for (age=bage; age<=fage; age ++){ 
     puts(line);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     fputs(line,ficparo);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   }      /* if (stepm >= YEARM) hstepm=1;*/
   ungetc(c,ficpar);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
    
   matcov=matrix(1,npar,1,npar);      /* If stepm=6 months */
   for(i=1; i <=npar; i++){      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     fscanf(ficpar,"%s",&str);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     if(mle==1)      
       printf("%s",str);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     fprintf(ficlog,"%s",str);  
     fprintf(ficparo,"%s",str);      /* Computing  Variances of health expectancies */
     for(j=1; j <=i; j++){      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
       fscanf(ficpar," %le",&matcov[i][j]);         decrease memory allocation */
       if(mle==1){      for(theta=1; theta <=npar; theta++){
         printf(" %.5le",matcov[i][j]);        for(i=1; i<=npar; i++){ 
         fprintf(ficlog," %.5le",matcov[i][j]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }          xm[i] = x[i] - (i==theta ?delti[theta]:0);
       else        }
         fprintf(ficlog," %.5le",matcov[i][j]);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       fprintf(ficparo," %.5le",matcov[i][j]);        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     }    
     fscanf(ficpar,"\n");        for(j=1; j<= nlstate; j++){
     if(mle==1)          for(i=1; i<=nlstate; i++){
       printf("\n");            for(h=0; h<=nhstepm-1; h++){
     fprintf(ficlog,"\n");              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     fprintf(ficparo,"\n");              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
   }            }
   for(i=1; i <=npar; i++)          }
     for(j=i+1;j<=npar;j++)        }
       matcov[i][j]=matcov[j][i];       
            for(ij=1; ij<= nlstate*nlstate; ij++)
   if(mle==1)          for(h=0; h<=nhstepm-1; h++){
     printf("\n");            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
   fprintf(ficlog,"\n");          }
       }/* End theta */
       
     /*-------- Rewriting paramater file ----------*/      
      strcpy(rfileres,"r");    /* "Rparameterfile */      for(h=0; h<=nhstepm-1; h++)
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        for(j=1; j<=nlstate*nlstate;j++)
      strcat(rfileres,".");    /* */          for(theta=1; theta <=npar; theta++)
      strcat(rfileres,optionfilext);    /* Other files have txt extension */            trgradg[h][j][theta]=gradg[h][theta][j];
     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;       for(ij=1;ij<=nlstate*nlstate;ij++)
     }        for(ji=1;ji<=nlstate*nlstate;ji++)
     fprintf(ficres,"#%s\n",version);          varhe[ij][ji][(int)age] =0.;
      
     /*-------- data file ----------*/       printf("%d|",(int)age);fflush(stdout);
     if((fic=fopen(datafile,"r"))==NULL)    {       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       printf("Problem with datafile: %s\n", datafile);goto end;       for(h=0;h<=nhstepm-1;h++){
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;        for(k=0;k<=nhstepm-1;k++){
     }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     n= lastobs;          for(ij=1;ij<=nlstate*nlstate;ij++)
     severity = vector(1,maxwav);            for(ji=1;ji<=nlstate*nlstate;ji++)
     outcome=imatrix(1,maxwav+1,1,n);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     num=ivector(1,n);        }
     moisnais=vector(1,n);      }
     annais=vector(1,n);  
     moisdc=vector(1,n);      /* Computing expectancies */
     andc=vector(1,n);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     agedc=vector(1,n);      for(i=1; i<=nlstate;i++)
     cod=ivector(1,n);        for(j=1; j<=nlstate;j++)
     weight=vector(1,n);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
     mint=matrix(1,maxwav,1,n);            
     anint=matrix(1,maxwav,1,n);            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);              }
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);      fprintf(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
     i=1;        eip=0.;
     while (fgets(line, MAXLINE, fic) != NULL)    {        vip=0.;
       if ((i >= firstobs) && (i <=lastobs)) {        for(j=1; j<=nlstate;j++){
                  eip += eij[i][j][(int)age];
         for (j=maxwav;j>=1;j--){          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           strcpy(line,stra);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        }
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
         }      }
              fprintf(ficresstdeij,"\n");
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        for(j=1; j<=nlstate;j++){
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);            for(j2=1; j2<=nlstate;j2++){
         for (j=ncovcol;j>=1;j--){              cptj2= (j2-1)*nlstate+i2;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);              if(cptj2 <= cptj)
         }                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
         num[i]=atol(stra);            }
                }
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      fprintf(ficrescveij,"\n");
           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;}*/     
     }
         i=i+1;    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       }    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     }    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     /* printf("ii=%d", ij);    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
        scanf("%d",i);*/    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   imx=i-1; /* Number of individuals */    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
   /* for (i=1; i<=imx; i++){    fprintf(ficlog,"\n");
     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;    free_vector(xm,1,npar);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    free_vector(xp,1,npar);
     }*/    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
    /*  for (i=1; i<=imx; i++){    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
      if (s[4][i]==9)  s[4][i]=-1;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
      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]));}*/  }
    
    /************ Variance ******************/
   /* Calculation of the number of parameter from char model*/  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[])
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */  {
   Tprod=ivector(1,15);    /* Variance of health expectancies */
   Tvaraff=ivector(1,15);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   Tvard=imatrix(1,15,1,2);    /* double **newm;*/
   Tage=ivector(1,15);          /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
        
   if (strlen(model) >1){    int movingaverage();
     j=0, j1=0, k1=1, k2=1;    double **dnewm,**doldm;
     j=nbocc(model,'+');    double **dnewmp,**doldmp;
     j1=nbocc(model,'*');    int i, j, nhstepm, hstepm, h, nstepm ;
     cptcovn=j+1;    int k;
     cptcovprod=j1;    double *xp;
        double **gp, **gm;  /* for var eij */
     strcpy(modelsav,model);    double ***gradg, ***trgradg; /*for var eij */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    double **gradgp, **trgradgp; /* for var p point j */
       printf("Error. Non available option model=%s ",model);    double *gpp, *gmp; /* for var p point j */
       fprintf(ficlog,"Error. Non available option model=%s ",model);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       goto end;    double ***p3mat;
     }    double age,agelim, hf;
        double ***mobaverage;
     for(i=(j+1); i>=1;i--){    int theta;
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */    char digit[4];
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */    char digitp[25];
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  
       /*scanf("%d",i);*/    char fileresprobmorprev[FILENAMELENGTH];
       if (strchr(strb,'*')) {  /* Model includes a product */  
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/    if(popbased==1){
         if (strcmp(strc,"age")==0) { /* Vn*age */      if(mobilav!=0)
           cptcovprod--;        strcpy(digitp,"-populbased-mobilav-");
           cutv(strb,stre,strd,'V');      else strcpy(digitp,"-populbased-nomobil-");
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/    }
           cptcovage++;    else 
             Tage[cptcovage]=i;      strcpy(digitp,"-stablbased-");
             /*printf("stre=%s ", stre);*/  
         }    if (mobilav!=0) {
         else if (strcmp(strd,"age")==0) { /* or age*Vn */      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           cptcovprod--;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           cutv(strb,stre,strc,'V');        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           Tvar[i]=atoi(stre);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           cptcovage++;      }
           Tage[cptcovage]=i;    }
         }  
         else {  /* Age is not in the model */    strcpy(fileresprobmorprev,"prmorprev"); 
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/    sprintf(digit,"%-d",ij);
           Tvar[i]=ncovcol+k1;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */    strcat(fileresprobmorprev,digit); /* Tvar to be done */
           Tprod[k1]=i;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           Tvard[k1][1]=atoi(strc); /* m*/    strcat(fileresprobmorprev,fileres);
           Tvard[k1][2]=atoi(stre); /* n */    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
           Tvar[cptcovn+k2]=Tvard[k1][1];      printf("Problem with resultfile: %s\n", fileresprobmorprev);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
           for (k=1; k<=lastobs;k++)    }
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           k1++;   
           k2=k2+2;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         }    pstamp(ficresprobmorprev);
       }    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
       else { /* no more sum */    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        /*  scanf("%d",i);*/      fprintf(ficresprobmorprev," p.%-d SE",j);
       cutv(strd,strc,strb,'V');      for(i=1; i<=nlstate;i++)
       Tvar[i]=atoi(strc);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       }    }  
       strcpy(modelsav,stra);      fprintf(ficresprobmorprev,"\n");
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    fprintf(ficgp,"\n# Routine varevsij");
         scanf("%d",i);*/    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     } /* end of loop + */    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");
   } /* end model */    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
    /*   } */
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   printf("cptcovprod=%d ", cptcovprod);    pstamp(ficresvij);
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
   scanf("%d ",i);*/    if(popbased==1)
     fclose(fic);      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     else
     /*  if(mle==1){*/      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     if (weightopt != 1) { /* Maximisation without weights*/    fprintf(ficresvij,"# Age");
       for(i=1;i<=n;i++) weight[i]=1.0;    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=nlstate;j++)
     /*-calculation of age at interview from date of interview and age at death -*/        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     agev=matrix(1,maxwav,1,imx);    fprintf(ficresvij,"\n");
   
     for (i=1; i<=imx; i++) {    xp=vector(1,npar);
       for(m=2; (m<= maxwav); m++) {    dnewm=matrix(1,nlstate,1,npar);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    doldm=matrix(1,nlstate,1,nlstate);
          anint[m][i]=9999;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
          s[m][i]=-1;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        }  
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       }    gpp=vector(nlstate+1,nlstate+ndeath);
     }    gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     for (i=1; i<=imx; i++)  {    
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    if(estepm < stepm){
       for(m=1; (m<= maxwav); m++){      printf ("Problem %d lower than %d\n",estepm, stepm);
         if(s[m][i] >0){    }
           if (s[m][i] >= nlstate+1) {    else  hstepm=estepm;   
             if(agedc[i]>0)    /* For example we decided to compute the life expectancy with the smallest unit */
               if(moisdc[i]!=99 && andc[i]!=9999)    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                 agev[m][i]=agedc[i];       nhstepm is the number of hstepm from age to agelim 
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/       nstepm is the number of stepm from age to agelin. 
            else {       Look at function hpijx to understand why (it is linked to memory size questions) */
               if (andc[i]!=9999){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
               printf("Warning negative age at death: %d line:%d\n",num[i],i);       survival function given by stepm (the optimization length). Unfortunately it
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);       means that if the survival funtion is printed every two years of age and if
               agev[m][i]=-1;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
               }       results. So we changed our mind and took the option of the best precision.
             }    */
           }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           else if(s[m][i] !=9){ /* Should no more exist */    agelim = AGESUP;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             if(mint[m][i]==99 || anint[m][i]==9999)      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
               agev[m][i]=1;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
             else if(agev[m][i] <agemin){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               agemin=agev[m][i];      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      gp=matrix(0,nhstepm,1,nlstate);
             }      gm=matrix(0,nhstepm,1,nlstate);
             else if(agev[m][i] >agemax){  
               agemax=agev[m][i];  
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      for(theta=1; theta <=npar; theta++){
             }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
             /*agev[m][i]=anint[m][i]-annais[i];*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             /*   agev[m][i] = age[i]+2*m;*/        }
           }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           else { /* =9 */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             agev[m][i]=1;  
             s[m][i]=-1;        if (popbased==1) {
           }          if(mobilav ==0){
         }            for(i=1; i<=nlstate;i++)
         else /*= 0 Unknown */              prlim[i][i]=probs[(int)age][i][ij];
           agev[m][i]=1;          }else{ /* mobilav */ 
       }            for(i=1; i<=nlstate;i++)
                  prlim[i][i]=mobaverage[(int)age][i][ij];
     }          }
     for (i=1; i<=imx; i++)  {        }
       for(m=1; (m<= maxwav); m++){    
         if (s[m][i] > (nlstate+ndeath)) {        for(j=1; j<= nlstate; j++){
           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);            for(h=0; h<=nhstepm; h++){
           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);              for(i=1, gp[h][j]=0.;i<=nlstate;i++)
           goto end;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
         }          }
       }        }
     }        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);           as a weighted average of prlim.
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
     free_vector(severity,1,maxwav);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     free_imatrix(outcome,1,maxwav+1,1,n);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     free_vector(moisnais,1,n);        }    
     free_vector(annais,1,n);        /* end probability of death */
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     free_vector(moisdc,1,n);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     free_vector(andc,1,n);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       
     wav=ivector(1,imx);        if (popbased==1) {
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          if(mobilav ==0){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);            for(i=1; i<=nlstate;i++)
                  prlim[i][i]=probs[(int)age][i][ij];
     /* Concatenates waves */          }else{ /* mobilav */ 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
       Tcode=ivector(1,100);        }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          for(h=0; h<=nhstepm; h++){
                  for(i=1, gm[h][j]=0.;i<=nlstate;i++)
    codtab=imatrix(1,100,1,10);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
    h=0;          }
    m=pow(2,cptcoveff);        }
          /* This for computing probability of death (h=1 means
    for(k=1;k<=cptcoveff; k++){           computed over hstepm matrices product = hstepm*stepm months) 
      for(i=1; i <=(m/pow(2,k));i++){           as a weighted average of prlim.
        for(j=1; j <= ncodemax[k]; j++){        */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
            h++;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;           gmp[j] += prlim[i][i]*p3mat[i][j][1];
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/        }    
          }        /* end probability of death */
        }  
      }        for(j=1; j<= nlstate; j++) /* vareij */
    }          for(h=0; h<=nhstepm; h++){
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       codtab[1][2]=1;codtab[2][2]=2; */          }
    /* for(i=1; i <=m ;i++){  
       for(k=1; k <=cptcovn; k++){        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       }        }
       printf("\n");  
       }      } /* End theta */
       scanf("%d",i);*/  
          trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
    /* Calculates basic frequencies. Computes observed prevalence at single age  
        and prints on file fileres'p'. */      for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
              for(theta=1; theta <=npar; theta++)
                trgradg[h][j][theta]=gradg[h][theta][j];
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(theta=1; theta <=npar; theta++)
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          trgradgp[j][theta]=gradgp[theta][j];
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    
        
     /* For Powell, parameters are in a vector p[] starting at p[1]      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      for(i=1;i<=nlstate;i++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      for(h=0;h<=nhstepm;h++){
     }        for(k=0;k<=nhstepm;k++){
              matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     /*--------- results files --------------*/          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     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);          for(i=1;i<=nlstate;i++)
              for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
    jk=1;        }
    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");      /* pptj */
    for(i=1,jk=1; i <=nlstate; i++){      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
      for(k=1; k <=(nlstate+ndeath); k++){      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
        if (k != i)      for(j=nlstate+1;j<=nlstate+ndeath;j++)
          {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
            printf("%d%d ",i,k);          varppt[j][i]=doldmp[j][i];
            fprintf(ficlog,"%d%d ",i,k);      /* end ppptj */
            fprintf(ficres,"%1d%1d ",i,k);      /*  x centered again */
            for(j=1; j <=ncovmodel; j++){      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
              printf("%f ",p[jk]);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
              fprintf(ficlog,"%f ",p[jk]);   
              fprintf(ficres,"%f ",p[jk]);      if (popbased==1) {
              jk++;        if(mobilav ==0){
            }          for(i=1; i<=nlstate;i++)
            printf("\n");            prlim[i][i]=probs[(int)age][i][ij];
            fprintf(ficlog,"\n");        }else{ /* mobilav */ 
            fprintf(ficres,"\n");          for(i=1; i<=nlstate;i++)
          }            prlim[i][i]=mobaverage[(int)age][i][ij];
      }        }
    }      }
    if(mle==1){               
      /* Computing hessian and covariance matrix */      /* This for computing probability of death (h=1 means
      ftolhess=ftol; /* Usually correct */         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
      hesscov(matcov, p, npar, delti, ftolhess, func);         as a weighted average of prlim.
    }      */
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      for(j=nlstate+1;j<=nlstate+ndeath;j++){
    printf("# Scales (for hessian or gradient estimation)\n");        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
    for(i=1,jk=1; i <=nlstate; i++){      }    
      for(j=1; j <=nlstate+ndeath; j++){      /* end probability of death */
        if (j!=i) {  
          fprintf(ficres,"%1d%1d",i,j);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
          printf("%1d%1d",i,j);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
          fprintf(ficlog,"%1d%1d",i,j);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
          for(k=1; k<=ncovmodel;k++){        for(i=1; i<=nlstate;i++){
            printf(" %.5e",delti[jk]);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
            fprintf(ficlog," %.5e",delti[jk]);        }
            fprintf(ficres," %.5e",delti[jk]);      } 
            jk++;      fprintf(ficresprobmorprev,"\n");
          }  
          printf("\n");      fprintf(ficresvij,"%.0f ",age );
          fprintf(ficlog,"\n");      for(i=1; i<=nlstate;i++)
          fprintf(ficres,"\n");        for(j=1; j<=nlstate;j++){
        }          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
      }        }
    }      fprintf(ficresvij,"\n");
          free_matrix(gp,0,nhstepm,1,nlstate);
    k=1;      free_matrix(gm,0,nhstepm,1,nlstate);
    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");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
    if(mle==1)      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
      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");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    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");    } /* End age */
    for(i=1;i<=npar;i++){    free_vector(gpp,nlstate+1,nlstate+ndeath);
      /*  if (k>nlstate) k=1;    free_vector(gmp,nlstate+1,nlstate+ndeath);
          i1=(i-1)/(ncovmodel*nlstate)+1;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
          printf("%s%d%d",alph[k],i1,tab[i]);*/    fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
      fprintf(ficres,"%3d",i);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
      if(mle==1)    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
        printf("%3d",i);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
      fprintf(ficlog,"%3d",i);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
      for(j=1; j<=i;j++){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
        fprintf(ficres," %.5e",matcov[i][j]);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
        if(mle==1)    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
          printf(" %.5e",matcov[i][j]);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
        fprintf(ficlog," %.5e",matcov[i][j]);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
      }    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
      fprintf(ficres,"\n");    /*  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);
      if(mle==1)  */
        printf("\n");  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
      fprintf(ficlog,"\n");    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
      k++;  
    }    free_vector(xp,1,npar);
        free_matrix(doldm,1,nlstate,1,nlstate);
    while((c=getc(ficpar))=='#' && c!= EOF){    free_matrix(dnewm,1,nlstate,1,npar);
      ungetc(c,ficpar);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      fgets(line, MAXLINE, ficpar);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
      puts(line);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      fputs(line,ficparo);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    }    fclose(ficresprobmorprev);
    ungetc(c,ficpar);    fflush(ficgp);
    estepm=0;    fflush(fichtm); 
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);  }  /* end varevsij */
    if (estepm==0 || estepm < stepm) estepm=stepm;  
    if (fage <= 2) {  /************ Variance of prevlim ******************/
      bage = ageminpar;  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[])
      fage = agemaxpar;  {
    }    /* Variance of prevalence limit */
        /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
    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);    double **dnewm,**doldm;
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    int i, j, nhstepm, hstepm;
        double *xp;
    while((c=getc(ficpar))=='#' && c!= EOF){    double *gp, *gm;
      ungetc(c,ficpar);    double **gradg, **trgradg;
      fgets(line, MAXLINE, ficpar);    double age,agelim;
      puts(line);    int theta;
      fputs(line,ficparo);    
    }    pstamp(ficresvpl);
    ungetc(c,ficpar);    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
      fprintf(ficresvpl,"# Age");
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    for(i=1; i<=nlstate;i++)
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        fprintf(ficresvpl," %1d-%1d",i,i);
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    fprintf(ficresvpl,"\n");
      
    while((c=getc(ficpar))=='#' && c!= EOF){    xp=vector(1,npar);
      ungetc(c,ficpar);    dnewm=matrix(1,nlstate,1,npar);
      fgets(line, MAXLINE, ficpar);    doldm=matrix(1,nlstate,1,nlstate);
      puts(line);    
      fputs(line,ficparo);    hstepm=1*YEARM; /* Every year of age */
    }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
    ungetc(c,ficpar);    agelim = AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      if (stepm >= YEARM) hstepm=1;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
   fscanf(ficpar,"pop_based=%d\n",&popbased);      gp=vector(1,nlstate);
   fprintf(ficparo,"pop_based=%d\n",popbased);        gm=vector(1,nlstate);
   fprintf(ficres,"pop_based=%d\n",popbased);    
        for(theta=1; theta <=npar; theta++){
   while((c=getc(ficpar))=='#' && c!= EOF){        for(i=1; i<=npar; i++){ /* Computes gradient */
     ungetc(c,ficpar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     fputs(line,ficparo);        for(i=1;i<=nlstate;i++)
   }          gp[i] = prlim[i][i];
   ungetc(c,ficpar);      
         for(i=1; i<=npar; i++) /* Computes gradient */
   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);          xp[i] = x[i] - (i==theta ?delti[theta]: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);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 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);        for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
 while((c=getc(ficpar))=='#' && c!= EOF){        for(i=1;i<=nlstate;i++)
     ungetc(c,ficpar);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     fgets(line, MAXLINE, ficpar);      } /* End theta */
     puts(line);  
     fputs(line,ficparo);      trgradg =matrix(1,nlstate,1,npar);
   }  
   ungetc(c,ficpar);      for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);          trgradg[j][theta]=gradg[theta][j];
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
 /*------------ gnuplot -------------*/      for(i=1;i<=nlstate;i++)
   strcpy(optionfilegnuplot,optionfilefiname);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   strcat(optionfilegnuplot,".gp");  
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      fprintf(ficresvpl,"%.0f ",age );
     printf("Problem with file %s",optionfilegnuplot);      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   fclose(ficgp);      fprintf(ficresvpl,"\n");
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);      free_vector(gp,1,nlstate);
 /*--------- index.htm --------*/      free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
   strcpy(optionfilehtm,optionfile);      free_matrix(trgradg,1,nlstate,1,npar);
   strcat(optionfilehtm,".htm");    } /* End age */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);    free_vector(xp,1,npar);
   }    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   fprintf(fichtm,"<body> <font size=\"2\">%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  
 Total number of observations=%d <br>\n  /************ Variance of one-step probabilities  ******************/
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n  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[])
 <hr  size=\"2\" color=\"#EC5E5E\">  {
  <ul><li><h4>Parameter files</h4>\n    int i, j=0,  k1, l1, tj;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    int k2, l2, j1,  z1;
  - Log file of the run: <a href=\"%s\">%s</a><br>\n    int k=0, l;
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);    int first=1, first1, first2;
   fclose(fichtm);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    double *xp;
      double *gp, *gm;
 /*------------ free_vector  -------------*/    double **gradg, **trgradg;
  chdir(path);    double **mu;
      double age, cov[NCOVMAX+1];
  free_ivector(wav,1,imx);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    int theta;
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      char fileresprob[FILENAMELENGTH];
  free_ivector(num,1,n);    char fileresprobcov[FILENAMELENGTH];
  free_vector(agedc,1,n);    char fileresprobcor[FILENAMELENGTH];
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    double ***varpij;
  fclose(ficparo);  
  fclose(ficres);    strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   /*--------------- Prevalence limit --------------*/      printf("Problem with resultfile: %s\n", fileresprob);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   strcpy(filerespl,"pl");    }
   strcat(filerespl,fileres);    strcpy(fileresprobcov,"probcov"); 
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    strcat(fileresprobcov,fileres);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;      printf("Problem with resultfile: %s\n", fileresprobcov);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    }
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);    strcpy(fileresprobcor,"probcor"); 
   fprintf(ficrespl,"#Prevalence limit\n");    strcat(fileresprobcor,fileres);
   fprintf(ficrespl,"#Age ");    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      printf("Problem with resultfile: %s\n", fileresprobcor);
   fprintf(ficrespl,"\n");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
      }
   prlim=matrix(1,nlstate,1,nlstate);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   k=0;    pstamp(ficresprob);
   agebase=ageminpar;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   agelim=agemaxpar;    fprintf(ficresprob,"# Age");
   ftolpl=1.e-10;    pstamp(ficresprobcov);
   i1=cptcoveff;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   if (cptcovn < 1){i1=1;}    fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficresprobcor,"# Age");
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");    for(i=1; i<=nlstate;i++)
         printf("\n#******");      for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficlog,"\n#******");        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         for(j=1;j<=cptcoveff;j++) {        fprintf(ficresprobcov," p%1d-%1d ",i,j);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      }  
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   /* fprintf(ficresprob,"\n");
         }    fprintf(ficresprobcov,"\n");
         fprintf(ficrespl,"******\n");    fprintf(ficresprobcor,"\n");
         printf("******\n");   */
         fprintf(ficlog,"******\n");    xp=vector(1,npar);
            dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         for (age=agebase; age<=agelim; age++){    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
           fprintf(ficrespl,"%.0f",age );    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
           for(i=1; i<=nlstate;i++)    first=1;
           fprintf(ficrespl," %.5f", prlim[i][i]);    fprintf(ficgp,"\n# Routine varprob");
           fprintf(ficrespl,"\n");    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);
   fclose(ficrespl);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
   /*------------- h Pij x at various ages ------------*/    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.\
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    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. \
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;  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>\
   printf("Computing pij: result on file '%s' \n", filerespij);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);   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");
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   /*if (stepm<=24) stepsize=2;*/    cov[1]=1;
     /* tj=cptcoveff; */
   agelim=AGESUP;    tj = (int) pow(2,cptcoveff);
   hstepm=stepsize*YEARM; /* Every year of age */    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    j1=0;
     for(j1=1; j1<=tj;j1++){
   /* hstepm=1;   aff par mois*/      /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
   k=0;        if  (cptcovn>0) {
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficresprob, "\n#********** Variable "); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       k=k+1;          fprintf(ficresprob, "**********\n#\n");
         fprintf(ficrespij,"\n#****** ");          fprintf(ficresprobcov, "\n#********** Variable "); 
         for(j=1;j<=cptcoveff;j++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficresprobcov, "**********\n#\n");
         fprintf(ficrespij,"******\n");          
                  fprintf(ficgp, "\n#********** Variable "); 
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          fprintf(ficgp, "**********\n#\n");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          
           
           /*      nhstepm=nhstepm*YEARM; aff par mois*/          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]]);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           oldm=oldms;savm=savms;          
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            fprintf(ficresprobcor, "\n#********** Variable ");    
           fprintf(ficrespij,"# Age");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for(i=1; i<=nlstate;i++)          fprintf(ficresprobcor, "**********\n#");    
             for(j=1; j<=nlstate+ndeath;j++)        }
               fprintf(ficrespij," %1d-%1d",i,j);        
           fprintf(ficrespij,"\n");        gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
            for (h=0; h<=nhstepm; h++){        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        gp=vector(1,(nlstate)*(nlstate+ndeath));
             for(i=1; i<=nlstate;i++)        gm=vector(1,(nlstate)*(nlstate+ndeath));
               for(j=1; j<=nlstate+ndeath;j++)        for (age=bage; age<=fage; age ++){ 
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          cov[2]=age;
             fprintf(ficrespij,"\n");          for (k=1; k<=cptcovn;k++) {
              }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                                           * 1  1 1 1 1
           fprintf(ficrespij,"\n");                                                           * 2  2 1 1 1
         }                                                           * 3  1 2 1 1
     }                                                           */
   }            /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
   fclose(ficrespij);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
   /*---------- Forecasting ------------------*/          for(theta=1; theta <=npar; theta++){
   if((stepm == 1) && (strcmp(model,".")==0)){            for(i=1; i<=npar; i++)
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);            
   }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   else{            
     erreur=108;            k=0;
     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(i=1; i<= (nlstate); i++){
     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);              for(j=1; j<=(nlstate+ndeath);j++){
   }                k=k+1;
                  gp[k]=pmmij[i][j];
               }
   /*---------- Health expectancies and variances ------------*/            }
             
   strcpy(filerest,"t");            for(i=1; i<=npar; i++)
   strcat(filerest,fileres);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   if((ficrest=fopen(filerest,"w"))==NULL) {      
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;            k=0;
   }            for(i=1; i<=(nlstate); i++){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);              for(j=1; j<=(nlstate+ndeath);j++){
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);                k=k+1;
                 gm[k]=pmmij[i][j];
               }
   strcpy(filerese,"e");            }
   strcat(filerese,fileres);       
   if((ficreseij=fopen(filerese,"w"))==NULL) {            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          }
   }  
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);            for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
   strcpy(fileresv,"v");          
   strcat(fileresv,fileres);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);          pmij(pmmij,cov,ncovmodel,x,nlstate);
   }          
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          k=0;
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          for(i=1; i<=(nlstate); i++){
   calagedate=-1;            for(j=1; j<=(nlstate+ndeath);j++){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              k=k+1;
               mu[k][(int) age]=pmmij[i][j];
   k=0;            }
   for(cptcov=1;cptcov<=i1;cptcov++){          }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
       k=k+1;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
       fprintf(ficrest,"\n#****** ");              varpij[i][j][(int)age] = doldm[i][j];
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          /*printf("\n%d ",(int)age);
       fprintf(ficrest,"******\n");            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(ficreseij,"\n#****** ");            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       for(j=1;j<=cptcoveff;j++)            }*/
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");          fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
       fprintf(ficresvij,"\n#****** ");          fprintf(ficresprobcor,"\n%d ",(int)age);
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       fprintf(ficresvij,"******\n");            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       oldm=oldms;savm=savms;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);            }
            i=0;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          for (k=1; k<=(nlstate);k++){
       oldm=oldms;savm=savms;            for (l=1; l<=(nlstate+ndeath);l++){ 
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);              i++;
       if(popbased==1){              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);              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(ficrest,"#Total LEs with variances: e.. (std) ");                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);              }
       fprintf(ficrest,"\n");            }
           }/* end of loop for state */
       epj=vector(1,nlstate+1);        } /* end of loop for age */
       for(age=bage; age <=fage ;age++){        free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         if (popbased==1) {        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);
             prlim[i][i]=probs[(int)age][i][k];        
         }        /* Confidence intervalle of pij  */
                /*
         fprintf(ficrest," %4.0f",age);          fprintf(ficgp,"\nunset parametric;unset label");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
             epj[j] += prlim[i][i]*eij[i][j][(int)age];          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);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           }          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           epj[nlstate+1] +=epj[j];          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         }        */
   
         for(i=1, vepp=0.;i <=nlstate;i++)        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
           for(j=1;j <=nlstate;j++)        first1=1;first2=2;
             vepp += vareij[i][j][(int)age];        for (k2=1; k2<=(nlstate);k2++){
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
         for(j=1;j <=nlstate;j++){            if(l2==k2) continue;
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));            j=(k2-1)*(nlstate+ndeath)+l2;
         }            for (k1=1; k1<=(nlstate);k1++){
         fprintf(ficrest,"\n");              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       }                if(l1==k1) continue;
     }                i=(k1-1)*(nlstate+ndeath)+l1;
   }                if(i<=j) continue;
 free_matrix(mint,1,maxwav,1,n);                for (age=bage; age<=fage; age ++){ 
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);                  if ((int)age %5==0){
     free_vector(weight,1,n);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   fclose(ficreseij);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   fclose(ficresvij);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   fclose(ficrest);                    mu1=mu[i][(int) age]/stepm*YEARM ;
   fclose(ficpar);                    mu2=mu[j][(int) age]/stepm*YEARM;
   free_vector(epj,1,nlstate+1);                    c12=cv12/sqrt(v1*v2);
                      /* Computing eigen value of matrix of covariance */
   /*------- Variance limit prevalence------*/                      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.;
   strcpy(fileresvpl,"vpl");                    if ((lc2 <0) || (lc1 <0) ){
   strcat(fileresvpl,fileres);                      if(first2==1){
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                        first1=0;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                      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);
     exit(0);                      }
   }                      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);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                      /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
   k=0;                    }
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    /* Eigen vectors */
       k=k+1;                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
       fprintf(ficresvpl,"\n#****** ");                    /*v21=sqrt(1.-v11*v11); *//* error */
       for(j=1;j<=cptcoveff;j++)                    v21=(lc1-v1)/cv12*v11;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    v12=-v21;
       fprintf(ficresvpl,"******\n");                    v22=v11;
                          tnalp=v21/v11;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);                    if(first1==1){
       oldm=oldms;savm=savms;                      first1=0;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                      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*/
   fclose(ficresvpl);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   /*---------- End : free ----------------*/                    if(first==1){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);                      first=0;
                        fprintf(ficgp,"\nset parametric;unset label");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                      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);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);                      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\">\
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                      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);
   free_matrix(matcov,1,npar,1,npar);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   free_vector(delti,1,npar);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   free_matrix(agev,1,maxwav,1,imx);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                      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),\
   fprintf(fichtm,"\n</body>");                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   fclose(fichtm);                    }else{
   fclose(ficgp);                      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);
   if(erreur >0){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     printf("End of Imach with error or warning %d\n",erreur);                      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",\
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   }else{                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
    printf("End of Imach\n");                    }/* if first */
    fprintf(ficlog,"End of Imach\n");                  } /* age mod 5 */
   }                } /* end loop age */
   printf("See log file on %s\n",filelog);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   fclose(ficlog);                first=1;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */              } /*l12 */
              } /* k12 */
   /* 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);*/          } /*l1 */
   /*printf("Total time was %d uSec.\n", total_usecs);*/        }/* k1 */
   /*------ End -----------*/        /* } */ /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
  end:    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
 #ifdef windows    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   /* chdir(pathcd);*/    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
 #endif    free_vector(xp,1,npar);
  /*system("wgnuplot graph.plt");*/    fclose(ficresprob);
  /*system("../gp37mgw/wgnuplot graph.plt");*/    fclose(ficresprobcov);
  /*system("cd ../gp37mgw");*/    fclose(ficresprobcor);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    fflush(ficgp);
  strcpy(plotcmd,GNUPLOTPROGRAM);    fflush(fichtmcov);
  strcat(plotcmd," ");  }
  strcat(plotcmd,optionfilegnuplot);  
  system(plotcmd);  
   /******************* Printing html file ***********/
 #ifdef windows  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   while (z[0] != 'q') {                    int lastpass, int stepm, int weightopt, char model[],\
     /* chdir(path); */                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");                    int popforecast, int estepm ,\
     scanf("%s",z);                    double jprev1, double mprev1,double anprev1, \
     if (z[0] == 'c') system("./imach");                    double jprev2, double mprev2,double anprev2){
     else if (z[0] == 'e') system(optionfilehtm);    int jj1, k1, i1, cpt;
     else if (z[0] == 'g') system(plotcmd);  
     else if (z[0] == 'q') exit(0);     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 \
 #endif  </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);
   }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
      /* #include <gnu/libc-version.h> */ /* Only on gnu */
   #include <stdint.h>
      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)
      printf("Windows (x64 and x86). ");fprintf(ficlog,"Windows (x64 and x86). ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix. ");fprintf(ficlog,"Unix. ");
   #elif __linux__
       // linux
      printf("linux. ");fprintf(ficlog,"linux. ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though...
      printf("Mac OS. ");fprintf(ficlog,"Mac OS. ");
   #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. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit.\n"); fprintf(ficlog," 32-bit.\n");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit.\n"); fprintf(ficlog," 64-bit.\n");/* 64-bit */
   #else
      printf(" wtf-bit.\n"); fprintf(ficlog," wtf-bit.\n");/* 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
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64())
              printf("The process is running under WOW64.\n");
      else
              printf("The process is not running under WOW64.\n");
   
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #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.1.50  
changed lines
  Added in v.1.173


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