Diff for /imach/src/imach.c between versions 1.50 and 1.183

version 1.50, 2002/06/26 23:25:02 version 1.183, 2015/03/10 20:34:32
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.183  2015/03/10 20:34:32  brouard
      Summary: 0.98q0, trying with directest, mnbrak fixed
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    We use directest instead of original Powell test; probably no
   first survey ("cross") where individuals from different ages are    incidence on the results, but better justifications;
   interviewed on their health status or degree of disability (in the    We fixed Numerical Recipes mnbrak routine which was wrong and gave
   case of a health survey which is our main interest) -2- at least a    wrong results.
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.182  2015/02/12 08:19:57  brouard
   computed from the time spent in each health state according to a    Summary: Trying to keep directest which seems simpler and more general
   model. More health states you consider, more time is necessary to reach the    Author: Nicolas Brouard
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.181  2015/02/11 23:22:24  brouard
   probability to be observed in state j at the second wave    Summary: Comments on Powell added
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Author:
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.180  2015/02/11 17:33:45  brouard
   where the markup *Covariates have to be included here again* invites    Summary: Finishing move from main to function (hpijx and prevalence_limit)
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.179  2015/01/04 09:57:06  brouard
     Summary: back to OS/X
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.178  2015/01/04 09:35:48  brouard
   identical for each individual. Also, if a individual missed an    *** empty log message ***
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.177  2015/01/03 18:40:56  brouard
     Summary: Still testing ilc32 on OSX
   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 1.176  2015/01/03 16:45:04  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 1.175  2015/01/03 16:33:42  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    *** empty log message ***
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.174  2015/01/03 16:15:49  brouard
     Summary: Still in cross-compilation
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.173  2015/01/03 12:06:26  brouard
      Summary: trying to detect cross-compilation
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.172  2014/12/27 12:07:47  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.171  2014/12/23 13:26:59  brouard
   software can be distributed freely for non commercial use. Latest version    Summary: Back from Visual C
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Still problem with utsname.h on Windows
    
 #include <math.h>    Revision 1.170  2014/12/23 11:17:12  brouard
 #include <stdio.h>    Summary: Cleaning some \%% back to %%
 #include <stdlib.h>  
 #include <unistd.h>    The escape was mandatory for a specific compiler (which one?), but too many warnings.
   
 #define MAXLINE 256    Revision 1.169  2014/12/22 23:08:31  brouard
 #define GNUPLOTPROGRAM "gnuplot"    Summary: 0.98p
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Outputs some informations on compiler used, OS etc. Testing on different platforms.
 /*#define DEBUG*/  
 #define windows    Revision 1.168  2014/12/22 15:17:42  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Summary: update
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.167  2014/12/22 13:50:56  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Summary: Testing uname and compiler version and if compiled 32 or 64
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Testing on Linux 64
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.166  2014/12/22 11:40:47  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    *** empty log message ***
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.165  2014/12/16 11:20:36  brouard
 #define YEARM 12. /* Number of months per year */    Summary: After compiling on Visual C
 #define AGESUP 130  
 #define AGEBASE 40    * imach.c (Module): Merging 1.61 to 1.162
 #ifdef windows  
 #define DIRSEPARATOR '\\'    Revision 1.164  2014/12/16 10:52:11  brouard
 #define ODIRSEPARATOR '/'    Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
 #else  
 #define DIRSEPARATOR '/'    * imach.c (Module): Merging 1.61 to 1.162
 #define ODIRSEPARATOR '\\'  
 #endif    Revision 1.163  2014/12/16 10:30:11  brouard
     * imach.c (Module): Merging 1.61 to 1.162
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";  
 int erreur; /* Error number */    Revision 1.162  2014/09/25 11:43:39  brouard
 int nvar;    Summary: temporary backup 0.99!
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.1  2014/09/16 11:06:58  brouard
 int nlstate=2; /* Number of live states */    Summary: With some code (wrong) for nlopt
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Author:
 int popbased=0;  
     Revision 1.161  2014/09/15 20:41:41  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    Summary: Problem with macro SQR on Intel compiler
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.160  2014/09/02 09:24:05  brouard
 int mle, weightopt;    *** empty log message ***
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.159  2014/09/01 10:34:10  brouard
 double jmean; /* Mean space between 2 waves */    Summary: WIN32
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Author: Brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.158  2014/08/27 17:11:51  brouard
 FILE *ficlog;    *** empty log message ***
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *ficresprobmorprev;    Revision 1.157  2014/08/27 16:26:55  brouard
 FILE *fichtm; /* Html File */    Summary: Preparing windows Visual studio version
 FILE *ficreseij;    Author: Brouard
 char filerese[FILENAMELENGTH];  
 FILE  *ficresvij;    In order to compile on Visual studio, time.h is now correct and time_t
 char fileresv[FILENAMELENGTH];    and tm struct should be used. difftime should be used but sometimes I
 FILE  *ficresvpl;    just make the differences in raw time format (time(&now).
 char fileresvpl[FILENAMELENGTH];    Trying to suppress #ifdef LINUX
 char title[MAXLINE];    Add xdg-open for __linux in order to open default browser.
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    Revision 1.156  2014/08/25 20:10:10  brouard
     *** empty log message ***
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
 char filelog[FILENAMELENGTH]; /* Log file */    Revision 1.155  2014/08/25 18:32:34  brouard
 char filerest[FILENAMELENGTH];    Summary: New compile, minor changes
 char fileregp[FILENAMELENGTH];    Author: Brouard
 char popfile[FILENAMELENGTH];  
     Revision 1.154  2014/06/20 17:32:08  brouard
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Summary: Outputs now all graphs of convergence to period prevalence
   
 #define NR_END 1    Revision 1.153  2014/06/20 16:45:46  brouard
 #define FREE_ARG char*    Summary: If 3 live state, convergence to period prevalence on same graph
 #define FTOL 1.0e-10    Author: Brouard
   
 #define NRANSI    Revision 1.152  2014/06/18 17:54:09  brouard
 #define ITMAX 200    Summary: open browser, use gnuplot on same dir than imach if not found in the path
   
 #define TOL 2.0e-4    Revision 1.151  2014/06/18 16:43:30  brouard
     *** empty log message ***
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.150  2014/06/18 16:42:35  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
     Author: brouard
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.149  2014/06/18 15:51:14  brouard
 #define TINY 1.0e-20    Summary: Some fixes in parameter files errors
     Author: Nicolas Brouard
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.148  2014/06/17 17:38:48  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Summary: Nothing new
      Author: Brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Just a new packaging for OS/X version 0.98nS
   
 static double sqrarg;    Revision 1.147  2014/06/16 10:33:11  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    *** empty log message ***
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Revision 1.146  2014/06/16 10:20:28  brouard
 int imx;    Summary: Merge
 int stepm;    Author: Brouard
 /* Stepm, step in month: minimum step interpolation*/  
     Merge, before building revised version.
 int estepm;  
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Revision 1.145  2014/06/10 21:23:15  brouard
     Summary: Debugging with valgrind
 int m,nb;    Author: Nicolas Brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Lot of changes in order to output the results with some covariates
 double **pmmij, ***probs, ***mobaverage;    After the Edimburgh REVES conference 2014, it seems mandatory to
 double dateintmean=0;    improve the code.
     No more memory valgrind error but a lot has to be done in order to
 double *weight;    continue the work of splitting the code into subroutines.
 int **s; /* Status */    Also, decodemodel has been improved. Tricode is still not
 double *agedc, **covar, idx;    optimal. nbcode should be improved. Documentation has been added in
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    the source code.
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Revision 1.143  2014/01/26 09:45:38  brouard
 double ftolhess; /* Tolerance for computing hessian */    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   
 /**************** split *************************/    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 {  
    char *s;                             /* pointer */    Revision 1.142  2014/01/26 03:57:36  brouard
    int  l1, l2;                         /* length counters */    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   
    l1 = strlen( path );                 /* length of path */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    Revision 1.141  2014/01/26 02:42:01  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)  
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    Revision 1.140  2011/09/02 10:37:54  brouard
 #if     defined(__bsd__)                /* get current working directory */    Summary: times.h is ok with mingw32 now.
       extern char       *getwd( );  
     Revision 1.139  2010/06/14 07:50:17  brouard
       if ( getwd( dirc ) == NULL ) {    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 #else    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
       extern char       *getcwd( );  
     Revision 1.138  2010/04/30 18:19:40  brouard
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    *** empty log message ***
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.137  2010/04/29 18:11:38  brouard
       }    (Module): Checking covariates for more complex models
       strcpy( name, path );             /* we've got it */    than V1+V2. A lot of change to be done. Unstable.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.136  2010/04/26 20:30:53  brouard
       l2 = strlen( s );                 /* length of filename */    (Module): merging some libgsl code. Fixing computation
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    of likelione (using inter/intrapolation if mle = 0) in order to
       strcpy( name, s );                /* save file name */    get same likelihood as if mle=1.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Some cleaning of code and comments added.
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.135  2009/10/29 15:33:14  brouard
    l1 = strlen( dirc );                 /* length of directory */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.134  2009/10/29 13:18:53  brouard
 #else    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.133  2009/07/06 10:21:25  brouard
    s = strrchr( name, '.' );            /* find last / */    just nforces
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.132  2009/07/06 08:22:05  brouard
    l1= strlen( name);    Many tings
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    Revision 1.131  2009/06/20 16:22:47  brouard
    finame[l1-l2]= 0;    Some dimensions resccaled
    return( 0 );                         /* we're done */  
 }    Revision 1.130  2009/05/26 06:44:34  brouard
     (Module): Max Covariate is now set to 20 instead of 8. A
     lot of cleaning with variables initialized to 0. Trying to make
 /******************************************/    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
 void replace(char *s, char*t)    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
   int i;  
   int lg=20;    Revision 1.128  2006/06/30 13:02:05  brouard
   i=0;    (Module): Clarifications on computing e.j
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.127  2006/04/28 18:11:50  brouard
     (s[i] = t[i]);    (Module): Yes the sum of survivors was wrong since
     if (t[i]== '\\') s[i]='/';    imach-114 because nhstepm was no more computed in the age
   }    loop. Now we define nhstepma in the age loop.
 }    (Module): In order to speed up (in case of numerous covariates) we
     compute health expectancies (without variances) in a first step
 int nbocc(char *s, char occ)    and then all the health expectancies with variances or standard
 {    deviation (needs data from the Hessian matrices) which slows the
   int i,j=0;    computation.
   int lg=20;    In the future we should be able to stop the program is only health
   i=0;    expectancies and graph are needed without standard deviations.
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.126  2006/04/28 17:23:28  brouard
   if  (s[i] == occ ) j++;    (Module): Yes the sum of survivors was wrong since
   }    imach-114 because nhstepm was no more computed in the age
   return j;    loop. Now we define nhstepma in the age loop.
 }    Version 0.98h
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.125  2006/04/04 15:20:31  lievre
 {    Errors in calculation of health expectancies. Age was not initialized.
   /* cuts string t into u and v where u is ended by char occ excluding it    Forecasting file added.
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)  
      gives u="abcedf" and v="ghi2j" */    Revision 1.124  2006/03/22 17:13:53  lievre
   int i,lg,j,p=0;    Parameters are printed with %lf instead of %f (more numbers after the comma).
   i=0;    The log-likelihood is printed in the log file
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Revision 1.123  2006/03/20 10:52:43  brouard
   }    * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
   lg=strlen(t);  
   for(j=0; j<p; j++) {    * imach.c (Module): Weights can have a decimal point as for
     (u[j] = t[j]);    English (a comma might work with a correct LC_NUMERIC environment,
   }    otherwise the weight is truncated).
      u[p]='\0';    Modification of warning when the covariates values are not 0 or
     1.
    for(j=0; j<= lg; j++) {    Version 0.98g
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.122  2006/03/20 09:45:41  brouard
 }    (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 /********************** nrerror ********************/    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 void nrerror(char error_text[])    1.
 {    Version 0.98g
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.121  2006/03/16 17:45:01  lievre
   exit(1);    * imach.c (Module): Comments concerning covariates added
 }  
 /*********************** vector *******************/    * imach.c (Module): refinements in the computation of lli if
 double *vector(int nl, int nh)    status=-2 in order to have more reliable computation if stepm is
 {    not 1 month. Version 0.98f
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.120  2006/03/16 15:10:38  lievre
   if (!v) nrerror("allocation failure in vector");    (Module): refinements in the computation of lli if
   return v-nl+NR_END;    status=-2 in order to have more reliable computation if stepm is
 }    not 1 month. Version 0.98f
   
 /************************ free vector ******************/    Revision 1.119  2006/03/15 17:42:26  brouard
 void free_vector(double*v, int nl, int nh)    (Module): Bug if status = -2, the loglikelihood was
 {    computed as likelihood omitting the logarithm. Version O.98e
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.118  2006/03/14 18:20:07  brouard
     (Module): varevsij Comments added explaining the second
 /************************ivector *******************************/    table of variances if popbased=1 .
 int *ivector(long nl,long nh)    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 {    (Module): Function pstamp added
   int *v;    (Module): Version 0.98d
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    Revision 1.117  2006/03/14 17:16:22  brouard
   return v-nl+NR_END;    (Module): varevsij Comments added explaining the second
 }    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 /******************free ivector **************************/    (Module): Function pstamp added
 void free_ivector(int *v, long nl, long nh)    (Module): Version 0.98d
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.116  2006/03/06 10:29:27  brouard
 }    (Module): Variance-covariance wrong links and
     varian-covariance of ej. is needed (Saito).
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Revision 1.115  2006/02/27 12:17:45  brouard
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    (Module): One freematrix added in mlikeli! 0.98c
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Revision 1.114  2006/02/26 12:57:58  brouard
   int **m;    (Module): Some improvements in processing parameter
      filename with strsep.
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Revision 1.113  2006/02/24 14:20:24  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Memory leaks checks with valgrind and:
   m += NR_END;    datafile was not closed, some imatrix were not freed and on matrix
   m -= nrl;    allocation too.
    
      Revision 1.112  2006/01/30 09:55:26  brouard
   /* allocate rows and set pointers to them */    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.111  2006/01/25 20:38:18  brouard
   m[nrl] += NR_END;    (Module): Lots of cleaning and bugs added (Gompertz)
   m[nrl] -= ncl;    (Module): Comments can be added in data file. Missing date values
      can be a simple dot '.'.
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
      Revision 1.110  2006/01/25 00:51:50  brouard
   /* return pointer to array of pointers to rows */    (Module): Lots of cleaning and bugs added (Gompertz)
   return m;  
 }    Revision 1.109  2006/01/24 19:37:15  brouard
     (Module): Comments (lines starting with a #) are allowed in data.
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    Revision 1.108  2006/01/19 18:05:42  lievre
       int **m;    Gnuplot problem appeared...
       long nch,ncl,nrh,nrl;    To be fixed
      /* free an int matrix allocated by imatrix() */  
 {    Revision 1.107  2006/01/19 16:20:37  brouard
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    Test existence of gnuplot in imach path
   free((FREE_ARG) (m+nrl-NR_END));  
 }    Revision 1.106  2006/01/19 13:24:36  brouard
     Some cleaning and links added in html output
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.105  2006/01/05 20:23:19  lievre
 {    *** empty log message ***
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    (Module): If the status is missing at the last wave but we know
   if (!m) nrerror("allocation failure 1 in matrix()");    that the person is alive, then we can code his/her status as -2
   m += NR_END;    (instead of missing=-1 in earlier versions) and his/her
   m -= nrl;    contributions to the likelihood is 1 - Prob of dying from last
     health status (= 1-p13= p11+p12 in the easiest case of somebody in
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    the healthy state at last known wave). Version is 0.98
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.103  2005/09/30 15:54:49  lievre
   m[nrl] -= ncl;    (Module): sump fixed, loop imx fixed, and simplifications.
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.102  2004/09/15 17:31:30  brouard
   return m;    Add the possibility to read data file including tab characters.
 }  
     Revision 1.101  2004/09/15 10:38:38  brouard
 /*************************free matrix ************************/    Fix on curr_time
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {    Revision 1.100  2004/07/12 18:29:06  brouard
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Add version for Mac OS X. Just define UNIX in Makefile
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Revision 1.98  2004/05/16 15:05:56  brouard
 {    New version 0.97 . First attempt to estimate force of mortality
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    directly from the data i.e. without the need of knowing the health
   double ***m;    state at each age, but using a Gompertz model: log u =a + b*age .
     This is the basic analysis of mortality and should be done before any
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    other analysis, in order to test if the mortality estimated from the
   if (!m) nrerror("allocation failure 1 in matrix()");    cross-longitudinal survey is different from the mortality estimated
   m += NR_END;    from other sources like vital statistic data.
   m -= nrl;  
     The same imach parameter file can be used but the option for mle should be -3.
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Agnès, who wrote this part of the code, tried to keep most of the
   m[nrl] += NR_END;    former routines in order to include the new code within the former code.
   m[nrl] -= ncl;  
     The output is very simple: only an estimate of the intercept and of
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    the slope with 95% confident intervals.
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Current limitations:
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    A) Even if you enter covariates, i.e. with the
   m[nrl][ncl] += NR_END;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   m[nrl][ncl] -= nll;    B) There is no computation of Life Expectancy nor Life Table.
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;    Revision 1.97  2004/02/20 13:25:42  lievre
      Version 0.96d. Population forecasting command line is (temporarily)
   for (i=nrl+1; i<=nrh; i++) {    suppressed.
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    Revision 1.96  2003/07/15 15:38:55  brouard
       m[i][j]=m[i][j-1]+nlay;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   }    rewritten within the same printf. Workaround: many printfs.
   return m;  
 }    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
 /*************************free ma3x ************************/    (Repository): Using imachwizard code to output a more meaningful covariance
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    matrix (cov(a12,c31) instead of numbers.
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    Revision 1.94  2003/06/27 13:00:02  brouard
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Just cleaning
   free((FREE_ARG)(m+nrl-NR_END));  
 }    Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 /***************** f1dim *************************/    exist so I changed back to asctime which exists.
 extern int ncom;    (Module): Version 0.96b
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);    Revision 1.92  2003/06/25 16:30:45  brouard
      (Module): On windows (cygwin) function asctime_r doesn't
 double f1dim(double x)    exist so I changed back to asctime which exists.
 {  
   int j;    Revision 1.91  2003/06/25 15:30:29  brouard
   double f;    * imach.c (Repository): Duplicated warning errors corrected.
   double *xt;    (Repository): Elapsed time after each iteration is now output. It
      helps to forecast when convergence will be reached. Elapsed time
   xt=vector(1,ncom);    is stamped in powell.  We created a new html file for the graphs
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    concerning matrix of covariance. It has extension -cov.htm.
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);    Revision 1.90  2003/06/24 12:34:15  brouard
   return f;    (Module): Some bugs corrected for windows. Also, when
 }    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    Revision 1.89  2003/06/24 12:30:52  brouard
 {    (Module): Some bugs corrected for windows. Also, when
   int iter;    mle=-1 a template is output in file "or"mypar.txt with the design
   double a,b,d,etemp;    of the covariance matrix to be input.
   double fu,fv,fw,fx;  
   double ftemp;    Revision 1.88  2003/06/23 17:54:56  brouard
   double p,q,r,tol1,tol2,u,v,w,x,xm;    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   double e=0.0;  
      Revision 1.87  2003/06/18 12:26:01  brouard
   a=(ax < cx ? ax : cx);    Version 0.96
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    Revision 1.86  2003/06/17 20:04:08  brouard
   fw=fv=fx=(*f)(x);    (Module): Change position of html and gnuplot routines and added
   for (iter=1;iter<=ITMAX;iter++) {    routine fileappend.
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    Revision 1.85  2003/06/17 13:12:43  brouard
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    * imach.c (Repository): Check when date of death was earlier that
     printf(".");fflush(stdout);    current date of interview. It may happen when the death was just
     fprintf(ficlog,".");fflush(ficlog);    prior to the death. In this case, dh was negative and likelihood
 #ifdef DEBUG    was wrong (infinity). We still send an "Error" but patch by
     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);    assuming that the date of death was just one stepm after the
     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);    interview.
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    (Repository): Because some people have very long ID (first column)
 #endif    we changed int to long in num[] and we added a new lvector for
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    memory allocation. But we also truncated to 8 characters (left
       *xmin=x;    truncation)
       return fx;    (Repository): No more line truncation errors.
     }  
     ftemp=fu;    Revision 1.84  2003/06/13 21:44:43  brouard
     if (fabs(e) > tol1) {    * imach.c (Repository): Replace "freqsummary" at a correct
       r=(x-w)*(fx-fv);    place. It differs from routine "prevalence" which may be called
       q=(x-v)*(fx-fw);    many times. Probs is memory consuming and must be used with
       p=(x-v)*q-(x-w)*r;    parcimony.
       q=2.0*(q-r);    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
       if (q > 0.0) p = -p;  
       q=fabs(q);    Revision 1.83  2003/06/10 13:39:11  lievre
       etemp=e;    *** empty log message ***
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    Revision 1.82  2003/06/05 15:57:20  brouard
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    Add log in  imach.c and  fullversion number is now printed.
       else {  
         d=p/q;  */
         u=x+d;  /*
         if (u-a < tol2 || b-u < tol2)     Interpolated Markov Chain
           d=SIGN(tol1,xm-x);  
       }    Short summary of the programme:
     } else {    
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    This program computes Healthy Life Expectancies from
     }    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    first survey ("cross") where individuals from different ages are
     fu=(*f)(u);    interviewed on their health status or degree of disability (in the
     if (fu <= fx) {    case of a health survey which is our main interest) -2- at least a
       if (u >= x) a=x; else b=x;    second wave of interviews ("longitudinal") which measure each change
       SHFT(v,w,x,u)    (if any) in individual health status.  Health expectancies are
         SHFT(fv,fw,fx,fu)    computed from the time spent in each health state according to a
         } else {    model. More health states you consider, more time is necessary to reach the
           if (u < x) a=u; else b=u;    Maximum Likelihood of the parameters involved in the model.  The
           if (fu <= fw || w == x) {    simplest model is the multinomial logistic model where pij is the
             v=w;    probability to be observed in state j at the second wave
             w=u;    conditional to be observed in state i at the first wave. Therefore
             fv=fw;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
             fw=fu;    'age' is age and 'sex' is a covariate. If you want to have a more
           } else if (fu <= fv || v == x || v == w) {    complex model than "constant and age", you should modify the program
             v=u;    where the markup *Covariates have to be included here again* invites
             fv=fu;    you to do it.  More covariates you add, slower the
           }    convergence.
         }  
   }    The advantage of this computer programme, compared to a simple
   nrerror("Too many iterations in brent");    multinomial logistic model, is clear when the delay between waves is not
   *xmin=x;    identical for each individual. Also, if a individual missed an
   return fx;    intermediate interview, the information is lost, but taken into
 }    account using an interpolation or extrapolation.  
   
 /****************** mnbrak ***********************/    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
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    split into an exact number (nh*stepm) of unobserved intermediate
             double (*func)(double))    states. This elementary transition (by month, quarter,
 {    semester or year) is modelled as a multinomial logistic.  The hPx
   double ulim,u,r,q, dum;    matrix is simply the matrix product of nh*stepm elementary matrices
   double fu;    and the contribution of each individual to the likelihood is simply
      hPijx.
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);    Also this programme outputs the covariance matrix of the parameters but also
   if (*fb > *fa) {    of the life expectancies. It also computes the period (stable) prevalence. 
     SHFT(dum,*ax,*bx,dum)    
       SHFT(dum,*fb,*fa,dum)    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
       }             Institut national d'études démographiques, Paris.
   *cx=(*bx)+GOLD*(*bx-*ax);    This software have been partly granted by Euro-REVES, a concerted action
   *fc=(*func)(*cx);    from the European Union.
   while (*fb > *fc) {    It is copyrighted identically to a GNU software product, ie programme and
     r=(*bx-*ax)*(*fb-*fc);    software can be distributed freely for non commercial use. Latest version
     q=(*bx-*cx)*(*fb-*fa);    can be accessed at http://euroreves.ined.fr/imach .
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     ulim=(*bx)+GLIMIT*(*cx-*bx);    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     if ((*bx-u)*(u-*cx) > 0.0) {    
       fu=(*func)(u);    **********************************************************************/
     } else if ((*cx-u)*(u-ulim) > 0.0) {  /*
       fu=(*func)(u);    main
       if (fu < *fc) {    read parameterfile
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    read datafile
           SHFT(*fb,*fc,fu,(*func)(u))    concatwav
           }    freqsummary
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    if (mle >= 1)
       u=ulim;      mlikeli
       fu=(*func)(u);    print results files
     } else {    if mle==1 
       u=(*cx)+GOLD*(*cx-*bx);       computes hessian
       fu=(*func)(u);    read end of parameter file: agemin, agemax, bage, fage, estepm
     }        begin-prev-date,...
     SHFT(*ax,*bx,*cx,u)    open gnuplot file
       SHFT(*fa,*fb,*fc,fu)    open html file
       }    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
 }     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
                                     | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
 /*************** linmin ************************/      freexexit2 possible for memory heap.
   
 int ncom;    h Pij x                         | pij_nom  ficrestpij
 double *pcom,*xicom;     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
 double (*nrfunc)(double []);         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
           1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   double brent(double ax, double bx, double cx,         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
                double (*f)(double), double tol, double *xmin);    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   double f1dim(double x);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
               double *fc, double (*func)(double));  
   int j;    forecasting if prevfcast==1 prevforecast call prevalence()
   double xx,xmin,bx,ax;    health expectancies
   double fx,fb,fa;    Variance-covariance of DFLE
      prevalence()
   ncom=n;     movingaverage()
   pcom=vector(1,n);    varevsij() 
   xicom=vector(1,n);    if popbased==1 varevsij(,popbased)
   nrfunc=func;    total life expectancies
   for (j=1;j<=n;j++) {    Variance of period (stable) prevalence
     pcom[j]=p[j];   end
     xicom[j]=xi[j];  */
   }  
   ax=0.0;  #define POWELL /* Instead of NLOPT */
   xx=1.0;  /* #define POWELLORIGINAL */ /* Don't use Directest to decide new direction but original Powell test */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #include <math.h>
 #ifdef DEBUG  #include <stdio.h>
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #include <stdlib.h>
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #include <string.h>
 #endif  
   for (j=1;j<=n;j++) {  #ifdef _WIN32
     xi[j] *= xmin;  #include <io.h>
     p[j] += xi[j];  #include <windows.h>
   }  #include <tchar.h>
   free_vector(xicom,1,n);  #else
   free_vector(pcom,1,n);  #include <unistd.h>
 }  #endif
   
 /*************** powell ************************/  #include <limits.h>
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  #include <sys/types.h>
             double (*func)(double []))  
 {  #if defined(__GNUC__)
   void linmin(double p[], double xi[], int n, double *fret,  #include <sys/utsname.h> /* Doesn't work on Windows */
               double (*func)(double []));  #endif
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  #include <sys/stat.h>
   double fp,fptt;  #include <errno.h>
   double *xits;  /* extern int errno; */
   pt=vector(1,n);  
   ptt=vector(1,n);  /* #ifdef LINUX */
   xit=vector(1,n);  /* #include <time.h> */
   xits=vector(1,n);  /* #include "timeval.h" */
   *fret=(*func)(p);  /* #else */
   for (j=1;j<=n;j++) pt[j]=p[j];  /* #include <sys/time.h> */
   for (*iter=1;;++(*iter)) {  /* #endif */
     fp=(*fret);  
     ibig=0;  #include <time.h>
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #ifdef GSL
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #include <gsl/gsl_errno.h>
     for (i=1;i<=n;i++)  #include <gsl/gsl_multimin.h>
       printf(" %d %.12f",i, p[i]);  #endif
     fprintf(ficlog," %d %.12f",i, p[i]);  
     printf("\n");  
     fprintf(ficlog,"\n");  #ifdef NLOPT
     for (i=1;i<=n;i++) {  #include <nlopt.h>
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  typedef struct {
       fptt=(*fret);    double (* function)(double [] );
 #ifdef DEBUG  } myfunc_data ;
       printf("fret=%lf \n",*fret);  #endif
       fprintf(ficlog,"fret=%lf \n",*fret);  
 #endif  /* #include <libintl.h> */
       printf("%d",i);fflush(stdout);  /* #define _(String) gettext (String) */
       fprintf(ficlog,"%d",i);fflush(ficlog);  
       linmin(p,xit,n,fret,func);  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       if (fabs(fptt-(*fret)) > del) {  
         del=fabs(fptt-(*fret));  #define GNUPLOTPROGRAM "gnuplot"
         ibig=i;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       }  #define FILENAMELENGTH 132
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       fprintf(ficlog,"%d %.12e",i,(*fret));  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
         printf(" x(%d)=%.12e",j,xit[j]);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  
       }  #define NINTERVMAX 8
       for(j=1;j<=n;j++) {  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
         printf(" p=%.12e",p[j]);  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
         fprintf(ficlog," p=%.12e",p[j]);  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
       }  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
       printf("\n");  #define MAXN 20000
       fprintf(ficlog,"\n");  #define YEARM 12. /**< Number of months per year */
 #endif  #define AGESUP 130
     }  #define AGEBASE 40
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
 #ifdef DEBUG  #ifdef _WIN32
       int k[2],l;  #define DIRSEPARATOR '\\'
       k[0]=1;  #define CHARSEPARATOR "\\"
       k[1]=-1;  #define ODIRSEPARATOR '/'
       printf("Max: %.12e",(*func)(p));  #else
       fprintf(ficlog,"Max: %.12e",(*func)(p));  #define DIRSEPARATOR '/'
       for (j=1;j<=n;j++) {  #define CHARSEPARATOR "/"
         printf(" %.12e",p[j]);  #define ODIRSEPARATOR '\\'
         fprintf(ficlog," %.12e",p[j]);  #endif
       }  
       printf("\n");  /* $Id$ */
       fprintf(ficlog,"\n");  /* $State$ */
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  char version[]="Imach version 0.98q0, March 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  char fullversion[]="$Revision$ $Date$"; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  char strstart[80];
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
         }  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  int nvar=0, nforce=0; /* Number of variables, number of forces */
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
       }  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
 #endif  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
   int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
       free_vector(xit,1,n);  int cptcovprodnoage=0; /**< Number of covariate products without age */   
       free_vector(xits,1,n);  int cptcoveff=0; /* Total number of covariates to vary for printing results */
       free_vector(ptt,1,n);  int cptcov=0; /* Working variable */
       free_vector(pt,1,n);  int npar=NPARMAX;
       return;  int nlstate=2; /* Number of live states */
     }  int ndeath=1; /* Number of dead states */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     for (j=1;j<=n;j++) {  int popbased=0;
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];  int *wav; /* Number of waves for this individuual 0 is possible */
       pt[j]=p[j];  int maxwav=0; /* Maxim number of waves */
     }  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
     fptt=(*func)(ptt);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
     if (fptt < fp) {  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);                     to the likelihood and the sum of weights (done by funcone)*/
       if (t < 0.0) {  int mle=1, weightopt=0;
         linmin(p,xit,n,fret,func);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
         for (j=1;j<=n;j++) {  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
           xi[j][ibig]=xi[j][n];  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
           xi[j][n]=xit[j];             * wave mi and wave mi+1 is not an exact multiple of stepm. */
         }  int countcallfunc=0;  /* Count the number of calls to func */
 #ifdef DEBUG  double jmean=1; /* Mean space between 2 waves */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  double **matprod2(); /* test */
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  double **oldm, **newm, **savm; /* Working pointers to matrices */
         for(j=1;j<=n;j++){  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
           printf(" %.12e",xit[j]);  /*FILE *fic ; */ /* Used in readdata only */
           fprintf(ficlog," %.12e",xit[j]);  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
         }  FILE *ficlog, *ficrespow;
         printf("\n");  int globpr=0; /* Global variable for printing or not */
         fprintf(ficlog,"\n");  double fretone; /* Only one call to likelihood */
 #endif  long ipmx=0; /* Number of contributions */
       }  double sw; /* Sum of weights */
     }  char filerespow[FILENAMELENGTH];
   }  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 }  FILE *ficresilk;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 /**** Prevalence limit ****************/  FILE *ficresprobmorprev;
   FILE *fichtm, *fichtmcov; /* Html File */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  FILE *ficresstdeij;
      matrix by transitions matrix until convergence is reached */  char fileresstde[FILENAMELENGTH];
   FILE *ficrescveij;
   int i, ii,j,k;  char filerescve[FILENAMELENGTH];
   double min, max, maxmin, maxmax,sumnew=0.;  FILE  *ficresvij;
   double **matprod2();  char fileresv[FILENAMELENGTH];
   double **out, cov[NCOVMAX], **pmij();  FILE  *ficresvpl;
   double **newm;  char fileresvpl[FILENAMELENGTH];
   double agefin, delaymax=50 ; /* Max number of years to converge */  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   for (ii=1;ii<=nlstate+ndeath;ii++)  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     for (j=1;j<=nlstate+ndeath;j++){  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  char command[FILENAMELENGTH];
     }  int  outcmd=0;
   
    cov[1]=1.;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
    
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  char filelog[FILENAMELENGTH]; /* Log file */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  char filerest[FILENAMELENGTH];
     newm=savm;  char fileregp[FILENAMELENGTH];
     /* Covariates have to be included here again */  char popfile[FILENAMELENGTH];
      cov[2]=agefin;  
    char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       for (k=1; k<=cptcovn;k++) {  
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
         /*      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]]);*/  /* struct timezone tzp; */
       }  /* extern int gettimeofday(); */
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  struct tm tml, *gmtime(), *localtime();
       for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  extern time_t time();
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  struct tm start_time, end_time, curr_time, last_time, forecast_time;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  struct tm tm;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
   char strcurr[80], strfor[80];
     savm=oldm;  
     oldm=newm;  char *endptr;
     maxmax=0.;  long lval;
     for(j=1;j<=nlstate;j++){  double dval;
       min=1.;  
       max=0.;  #define NR_END 1
       for(i=1; i<=nlstate; i++) {  #define FREE_ARG char*
         sumnew=0;  #define FTOL 1.0e-10
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  #define NRANSI 
         max=FMAX(max,prlim[i][j]);  #define ITMAX 200 
         min=FMIN(min,prlim[i][j]);  
       }  #define TOL 2.0e-4 
       maxmin=max-min;  
       maxmax=FMAX(maxmax,maxmin);  #define CGOLD 0.3819660 
     }  #define ZEPS 1.0e-10 
     if(maxmax < ftolpl){  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       return prlim;  
     }  #define GOLD 1.618034 
   }  #define GLIMIT 100.0 
 }  #define TINY 1.0e-20 
   
 /*************** transition probabilities ***************/  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 {    
   double s1, s2;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   /*double t34;*/  #define rint(a) floor(a+0.5)
   int i,j,j1, nc, ii, jj;  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
   #define mytinydouble 1.0e-16
     for(i=1; i<= nlstate; i++){  /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
     for(j=1; j<i;j++){  /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /* static double dsqrarg; */
         /*s2 += param[i][j][nc]*cov[nc];*/  /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  static double sqrarg;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       ps[i][j]=s2;  int agegomp= AGEGOMP;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  int imx; 
     for(j=i+1; j<=nlstate+ndeath;j++){  int stepm=1;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /* Stepm, step in month: minimum step interpolation*/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  int estepm;
       }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       ps[i][j]=s2;  
     }  int m,nb;
   }  long *num;
     /*ps[3][2]=1;*/  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   for(i=1; i<= nlstate; i++){  double **pmmij, ***probs;
      s1=0;  double *ageexmed,*agecens;
     for(j=1; j<i; j++)  double dateintmean=0;
       s1+=exp(ps[i][j]);  
     for(j=i+1; j<=nlstate+ndeath; j++)  double *weight;
       s1+=exp(ps[i][j]);  int **s; /* Status */
     ps[i][i]=1./(s1+1.);  double *agedc;
     for(j=1; j<i; j++)  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
       ps[i][j]= exp(ps[i][j])*ps[i][i];                    * covar=matrix(0,NCOVMAX,1,n); 
     for(j=i+1; j<=nlstate+ndeath; j++)                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       ps[i][j]= exp(ps[i][j])*ps[i][i];  double  idx; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   } /* end i */  int *Ndum; /** Freq of modality (tricode */
   int **codtab; /**< codtab=imatrix(1,100,1,10); */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
     for(jj=1; jj<= nlstate+ndeath; jj++){  double *lsurv, *lpop, *tpop;
       ps[ii][jj]=0;  
       ps[ii][ii]=1;  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
     }  double ftolhess; /**< Tolerance for computing hessian */
   }  
   /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  {
     for(jj=1; jj<= nlstate+ndeath; jj++){    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
      printf("%lf ",ps[ii][jj]);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
    }    */ 
     printf("\n ");    char  *ss;                            /* pointer */
     }    int   l1, l2;                         /* length counters */
     printf("\n ");printf("%lf ",cov[2]);*/  
 /*    l1 = strlen(path );                   /* length of path */
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   goto end;*/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     return ps;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
 }      strcpy( name, path );               /* we got the fullname name because no directory */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 /**************** Product of 2 matrices ******************/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       /* get current working directory */
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      /*    extern  char* getcwd ( char *buf , int len);*/
 {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        return( GLOCK_ERROR_GETCWD );
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      }
   /* in, b, out are matrice of pointers which should have been initialized      /* got dirc from getcwd*/
      before: only the contents of out is modified. The function returns      printf(" DIRC = %s \n",dirc);
      a pointer to pointers identical to out */    } else {                              /* strip direcotry from path */
   long i, j, k;      ss++;                               /* after this, the filename */
   for(i=nrl; i<= nrh; i++)      l2 = strlen( ss );                  /* length of filename */
     for(k=ncolol; k<=ncoloh; k++)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      strcpy( name, ss );         /* save file name */
         out[i][k] +=in[i][j]*b[j][k];      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
   return out;      printf(" DIRC2 = %s \n",dirc);
 }    }
     /* We add a separator at the end of dirc if not exists */
     l1 = strlen( dirc );                  /* length of directory */
 /************* Higher Matrix Product ***************/    if( dirc[l1-1] != DIRSEPARATOR ){
       dirc[l1] =  DIRSEPARATOR;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      dirc[l1+1] = 0; 
 {      printf(" DIRC3 = %s \n",dirc);
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    }
      duration (i.e. until    ss = strrchr( name, '.' );            /* find last / */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    if (ss >0){
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      ss++;
      (typically every 2 years instead of every month which is too big).      strcpy(ext,ss);                     /* save extension */
      Model is determined by parameters x and covariates have to be      l1= strlen( name);
      included manually here.      l2= strlen(ss)+1;
       strncpy( finame, name, l1-l2);
      */      finame[l1-l2]= 0;
     }
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];    return( 0 );                          /* we're done */
   double **newm;  }
   
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)  /******************************************/
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);  void replace_back_to_slash(char *s, char*t)
       po[i][j][0]=(i==j ? 1.0 : 0.0);  {
     }    int i;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    int lg=0;
   for(h=1; h <=nhstepm; h++){    i=0;
     for(d=1; d <=hstepm; d++){    lg=strlen(t);
       newm=savm;    for(i=0; i<= lg; i++) {
       /* Covariates have to be included here again */      (s[i] = t[i]);
       cov[1]=1.;      if (t[i]== '\\') s[i]='/';
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    }
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  }
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  char *trimbb(char *out, char *in)
       for (k=1; k<=cptcovprod;k++)  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    char *s;
     s=out;
     while (*in != '\0'){
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        in++;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      *out++ = *in++;
       savm=oldm;    }
       oldm=newm;    *out='\0';
     }    return s;
     for(i=1; i<=nlstate+ndeath; i++)  }
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];  char *cutl(char *blocc, char *alocc, char *in, char occ)
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  {
          */    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
       }       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   } /* end h */       gives blocc="abcdef2ghi" and alocc="j".
   return po;       If occ is not found blocc is null and alocc is equal to in. Returns blocc
 }    */
     char *s, *t;
     t=in;s=in;
 /*************** log-likelihood *************/    while ((*in != occ) && (*in != '\0')){
 double func( double *x)      *alocc++ = *in++;
 {    }
   int i, ii, j, k, mi, d, kk;    if( *in == occ){
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      *(alocc)='\0';
   double **out;      s=++in;
   double sw; /* Sum of weights */    }
   double lli; /* Individual log likelihood */   
   long ipmx;    if (s == t) {/* occ not found */
   /*extern weight */      *(alocc-(in-s))='\0';
   /* We are differentiating ll according to initial status */      in=s;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    }
   /*for(i=1;i<imx;i++)    while ( *in != '\0'){
     printf(" %d\n",s[4][i]);      *blocc++ = *in++;
   */    }
   cov[1]=1.;  
     *blocc='\0';
   for(k=1; k<=nlstate; k++) ll[k]=0.;    return t;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  }
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  char *cutv(char *blocc, char *alocc, char *in, char occ)
     for(mi=1; mi<= wav[i]-1; mi++){  {
       for (ii=1;ii<=nlstate+ndeath;ii++)    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       for(d=0; d<dh[mi][i]; d++){       gives blocc="abcdef2ghi" and alocc="j".
         newm=savm;       If occ is not found blocc is null and alocc is equal to in. Returns alocc
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    */
         for (kk=1; kk<=cptcovage;kk++) {    char *s, *t;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    t=in;s=in;
         }    while (*in != '\0'){
              while( *in == occ){
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        *blocc++ = *in++;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        s=in;
         savm=oldm;      }
         oldm=newm;      *blocc++ = *in++;
            }
            if (s == t) /* occ not found */
       } /* end mult */      *(blocc-(in-s))='\0';
          else
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      *(blocc-(in-s)-1)='\0';
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    in=s;
       ipmx +=1;    while ( *in != '\0'){
       sw += weight[i];      *alocc++ = *in++;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    }
     } /* end of wave */  
   } /* end of individual */    *alocc='\0';
     return s;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  }
   /* 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 nbocc(char *s, char occ)
   return -l;  {
 }    int i,j=0;
     int lg=20;
     i=0;
 /*********** Maximum Likelihood Estimation ***************/    lg=strlen(s);
     for(i=0; i<= lg; i++) {
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    if  (s[i] == occ ) j++;
 {    }
   int i,j, iter;    return j;
   double **xi,*delti;  }
   double fret;  
   xi=matrix(1,npar,1,npar);  /* void cutv(char *u,char *v, char*t, char occ) */
   for (i=1;i<=npar;i++)  /* { */
     for (j=1;j<=npar;j++)  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
       xi[i][j]=(i==j ? 1.0 : 0.0);  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   printf("Powell\n");  fprintf(ficlog,"Powell\n");  /*      gives u="abcdef2ghi" and v="j" *\/ */
   powell(p,xi,npar,ftol,&iter,&fret,func);  /*   int i,lg,j,p=0; */
   /*   i=0; */
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  /*   lg=strlen(t); */
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  /*   for(j=0; j<=lg-1; j++) { */
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   /*   } */
 }  
   /*   for(j=0; j<p; j++) { */
 /**** Computes Hessian and covariance matrix ***/  /*     (u[j] = t[j]); */
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /*   } */
 {  /*      u[p]='\0'; */
   double  **a,**y,*x,pd;  
   double **hess;  /*    for(j=0; j<= lg; j++) { */
   int i, j,jk;  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   int *indx;  /*   } */
   /* } */
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);  #ifdef _WIN32
   void lubksb(double **a, int npar, int *indx, double b[]) ;  char * strsep(char **pp, const char *delim)
   void ludcmp(double **a, int npar, int *indx, double *d) ;  {
     char *p, *q;
   hess=matrix(1,npar,1,npar);           
     if ((p = *pp) == NULL)
   printf("\nCalculation of the hessian matrix. Wait...\n");      return 0;
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");    if ((q = strpbrk (p, delim)) != NULL)
   for (i=1;i<=npar;i++){    {
     printf("%d",i);fflush(stdout);      *pp = q + 1;
     fprintf(ficlog,"%d",i);fflush(ficlog);      *q = '\0';
     hess[i][i]=hessii(p,ftolhess,i,delti);    }
     /*printf(" %f ",p[i]);*/    else
     /*printf(" %lf ",hess[i][i]);*/      *pp = 0;
   }    return p;
    }
   for (i=1;i<=npar;i++) {  #endif
     for (j=1;j<=npar;j++)  {  
       if (j>i) {  /********************** nrerror ********************/
         printf(".%d%d",i,j);fflush(stdout);  
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);  void nrerror(char error_text[])
         hess[i][j]=hessij(p,delti,i,j);  {
         hess[j][i]=hess[i][j];        fprintf(stderr,"ERREUR ...\n");
         /*printf(" %lf ",hess[i][j]);*/    fprintf(stderr,"%s\n",error_text);
       }    exit(EXIT_FAILURE);
     }  }
   }  /*********************** vector *******************/
   printf("\n");  double *vector(int nl, int nh)
   fprintf(ficlog,"\n");  {
     double *v;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    if (!v) nrerror("allocation failure in vector");
      return v-nl+NR_END;
   a=matrix(1,npar,1,npar);  }
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);  /************************ free vector ******************/
   indx=ivector(1,npar);  void free_vector(double*v, int nl, int nh)
   for (i=1;i<=npar;i++)  {
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    free((FREE_ARG)(v+nl-NR_END));
   ludcmp(a,npar,indx,&pd);  }
   
   for (j=1;j<=npar;j++) {  /************************ivector *******************************/
     for (i=1;i<=npar;i++) x[i]=0;  int *ivector(long nl,long nh)
     x[j]=1;  {
     lubksb(a,npar,indx,x);    int *v;
     for (i=1;i<=npar;i++){    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       matcov[i][j]=x[i];    if (!v) nrerror("allocation failure in ivector");
     }    return v-nl+NR_END;
   }  }
   
   printf("\n#Hessian matrix#\n");  /******************free ivector **************************/
   fprintf(ficlog,"\n#Hessian matrix#\n");  void free_ivector(int *v, long nl, long nh)
   for (i=1;i<=npar;i++) {  {
     for (j=1;j<=npar;j++) {    free((FREE_ARG)(v+nl-NR_END));
       printf("%.3e ",hess[i][j]);  }
       fprintf(ficlog,"%.3e ",hess[i][j]);  
     }  /************************lvector *******************************/
     printf("\n");  long *lvector(long nl,long nh)
     fprintf(ficlog,"\n");  {
   }    long *v;
     v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   /* Recompute Inverse */    if (!v) nrerror("allocation failure in ivector");
   for (i=1;i<=npar;i++)    return v-nl+NR_END;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  }
   ludcmp(a,npar,indx,&pd);  
   /******************free lvector **************************/
   /*  printf("\n#Hessian matrix recomputed#\n");  void free_lvector(long *v, long nl, long nh)
   {
   for (j=1;j<=npar;j++) {    free((FREE_ARG)(v+nl-NR_END));
     for (i=1;i<=npar;i++) x[i]=0;  }
     x[j]=1;  
     lubksb(a,npar,indx,x);  /******************* imatrix *******************************/
     for (i=1;i<=npar;i++){  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       y[i][j]=x[i];       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       printf("%.3e ",y[i][j]);  { 
       fprintf(ficlog,"%.3e ",y[i][j]);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     }    int **m; 
     printf("\n");    
     fprintf(ficlog,"\n");    /* allocate pointers to rows */ 
   }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   */    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
   free_matrix(a,1,npar,1,npar);    m -= nrl; 
   free_matrix(y,1,npar,1,npar);    
   free_vector(x,1,npar);    
   free_ivector(indx,1,npar);    /* allocate rows and set pointers to them */ 
   free_matrix(hess,1,npar,1,npar);    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; 
 }    m[nrl] -= ncl; 
     
 /*************** hessian matrix ****************/    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 double hessii( double x[], double delta, int theta, double delti[])    
 {    /* return pointer to array of pointers to rows */ 
   int i;    return m; 
   int l=1, lmax=20;  } 
   double k1,k2;  
   double p2[NPARMAX+1];  /****************** free_imatrix *************************/
   double res;  void free_imatrix(m,nrl,nrh,ncl,nch)
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        int **m;
   double fx;        long nch,ncl,nrh,nrl; 
   int k=0,kmax=10;       /* free an int matrix allocated by imatrix() */ 
   double l1;  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   fx=func(x);    free((FREE_ARG) (m+nrl-NR_END)); 
   for (i=1;i<=npar;i++) p2[i]=x[i];  } 
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);  /******************* matrix *******************************/
     delts=delt;  double **matrix(long nrl, long nrh, long ncl, long nch)
     for(k=1 ; k <kmax; k=k+1){  {
       delt = delta*(l1*k);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       p2[theta]=x[theta] +delt;    double **m;
       k1=func(p2)-fx;  
       p2[theta]=x[theta]-delt;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       k2=func(p2)-fx;    if (!m) nrerror("allocation failure 1 in matrix()");
       /*res= (k1-2.0*fx+k2)/delt/delt; */    m += NR_END;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    m -= nrl;
        
 #ifdef DEBUG    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       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);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       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] += NR_END;
 #endif    m[nrl] -= ncl;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         k=kmax;    return m;
       }    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
         k=kmax; l=lmax*10.;  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
       }     */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  }
         delts=delt;  
       }  /*************************free matrix ************************/
     }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   }  {
   delti[theta]=delts;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   return res;    free((FREE_ARG)(m+nrl-NR_END));
    }
 }  
   /******************* ma3x *******************************/
 double hessij( double x[], double delti[], int thetai,int thetaj)  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 {  {
   int i;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   int l=1, l1, lmax=20;    double ***m;
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   int k;    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
   fx=func(x);    m -= nrl;
   for (k=1; k<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     p2[thetai]=x[thetai]+delti[thetai]/k;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    m[nrl] += NR_END;
     k1=func(p2)-fx;    m[nrl] -= ncl;
    
     p2[thetai]=x[thetai]+delti[thetai]/k;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
      if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     p2[thetai]=x[thetai]-delti[thetai]/k;    m[nrl][ncl] += NR_END;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    m[nrl][ncl] -= nll;
     k3=func(p2)-fx;    for (j=ncl+1; j<=nch; j++) 
        m[nrl][j]=m[nrl][j-1]+nlay;
     p2[thetai]=x[thetai]-delti[thetai]/k;    
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    for (i=nrl+1; i<=nrh; i++) {
     k4=func(p2)-fx;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      for (j=ncl+1; j<=nch; j++) 
 #ifdef DEBUG        m[i][j]=m[i][j-1]+nlay;
     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);    return m; 
 #endif    /*  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)
   return res;    */
 }  }
   
 /************** Inverse of matrix **************/  /*************************free ma3x ************************/
 void ludcmp(double **a, int n, int *indx, double *d)  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 {  {
   int i,imax,j,k;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   double big,dum,sum,temp;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double *vv;    free((FREE_ARG)(m+nrl-NR_END));
    }
   vv=vector(1,n);  
   *d=1.0;  /*************** function subdirf ***********/
   for (i=1;i<=n;i++) {  char *subdirf(char fileres[])
     big=0.0;  {
     for (j=1;j<=n;j++)    /* Caution optionfilefiname is hidden */
       if ((temp=fabs(a[i][j])) > big) big=temp;    strcpy(tmpout,optionfilefiname);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    strcat(tmpout,"/"); /* Add to the right */
     vv[i]=1.0/big;    strcat(tmpout,fileres);
   }    return tmpout;
   for (j=1;j<=n;j++) {  }
     for (i=1;i<j;i++) {  
       sum=a[i][j];  /*************** function subdirf2 ***********/
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  char *subdirf2(char fileres[], char *preop)
       a[i][j]=sum;  {
     }    
     big=0.0;    /* Caution optionfilefiname is hidden */
     for (i=j;i<=n;i++) {    strcpy(tmpout,optionfilefiname);
       sum=a[i][j];    strcat(tmpout,"/");
       for (k=1;k<j;k++)    strcat(tmpout,preop);
         sum -= a[i][k]*a[k][j];    strcat(tmpout,fileres);
       a[i][j]=sum;    return tmpout;
       if ( (dum=vv[i]*fabs(sum)) >= big) {  }
         big=dum;  
         imax=i;  /*************** function subdirf3 ***********/
       }  char *subdirf3(char fileres[], char *preop, char *preop2)
     }  {
     if (j != imax) {    
       for (k=1;k<=n;k++) {    /* Caution optionfilefiname is hidden */
         dum=a[imax][k];    strcpy(tmpout,optionfilefiname);
         a[imax][k]=a[j][k];    strcat(tmpout,"/");
         a[j][k]=dum;    strcat(tmpout,preop);
       }    strcat(tmpout,preop2);
       *d = -(*d);    strcat(tmpout,fileres);
       vv[imax]=vv[j];    return tmpout;
     }  }
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  char *asc_diff_time(long time_sec, char ascdiff[])
     if (j != n) {  {
       dum=1.0/(a[j][j]);    long sec_left, days, hours, minutes;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    days = (time_sec) / (60*60*24);
     }    sec_left = (time_sec) % (60*60*24);
   }    hours = (sec_left) / (60*60) ;
   free_vector(vv,1,n);  /* Doesn't work */    sec_left = (sec_left) %(60*60);
 ;    minutes = (sec_left) /60;
 }    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
 void lubksb(double **a, int n, int *indx, double b[])    return ascdiff;
 {  }
   int i,ii=0,ip,j;  
   double sum;  /***************** f1dim *************************/
    extern int ncom; 
   for (i=1;i<=n;i++) {  extern double *pcom,*xicom;
     ip=indx[i];  extern double (*nrfunc)(double []); 
     sum=b[ip];   
     b[ip]=b[i];  double f1dim(double x) 
     if (ii)  { 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    int j; 
     else if (sum) ii=i;    double f;
     b[i]=sum;    double *xt; 
   }   
   for (i=n;i>=1;i--) {    xt=vector(1,ncom); 
     sum=b[i];    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    f=(*nrfunc)(xt); 
     b[i]=sum/a[i][i];    free_vector(xt,1,ncom); 
   }    return f; 
 }  } 
   
 /************ Frequencies ********************/  /*****************brent *************************/
 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)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
 {  /* Some frequencies */  { 
      int iter; 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    double a,b,d,etemp;
   int first;    double fu=0,fv,fw,fx;
   double ***freq; /* Frequencies */    double ftemp=0.;
   double *pp;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   double pos, k2, dateintsum=0,k2cpt=0;    double e=0.0; 
   FILE *ficresp;   
   char fileresp[FILENAMELENGTH];    a=(ax < cx ? ax : cx); 
      b=(ax > cx ? ax : cx); 
   pp=vector(1,nlstate);    x=w=v=bx; 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    fw=fv=fx=(*f)(x); 
   strcpy(fileresp,"p");    for (iter=1;iter<=ITMAX;iter++) { 
   strcat(fileresp,fileres);      xm=0.5*(a+b); 
   if((ficresp=fopen(fileresp,"w"))==NULL) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     printf("Problem with prevalence resultfile: %s\n", fileresp);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);      printf(".");fflush(stdout);
     exit(0);      fprintf(ficlog,".");fflush(ficlog);
   }  #ifdef DEBUGBRENT
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      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);
   j1=0;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
        /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   j=cptcoveff;  #endif
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
   first=1;        return fx; 
       } 
   for(k1=1; k1<=j;k1++){      ftemp=fu;
     for(i1=1; i1<=ncodemax[k1];i1++){      if (fabs(e) > tol1) { 
       j1++;        r=(x-w)*(fx-fv); 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        q=(x-v)*(fx-fw); 
         scanf("%d", i);*/        p=(x-v)*q-(x-w)*r; 
       for (i=-1; i<=nlstate+ndeath; i++)          q=2.0*(q-r); 
         for (jk=-1; jk<=nlstate+ndeath; jk++)          if (q > 0.0) p = -p; 
           for(m=agemin; m <= agemax+3; m++)        q=fabs(q); 
             freq[i][jk][m]=0;        etemp=e; 
              e=d; 
       dateintsum=0;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       k2cpt=0;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for (i=1; i<=imx; i++) {        else { 
         bool=1;          d=p/q; 
         if  (cptcovn>0) {          u=x+d; 
           for (z1=1; z1<=cptcoveff; z1++)          if (u-a < tol2 || b-u < tol2) 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            d=SIGN(tol1,xm-x); 
               bool=0;        } 
         }      } else { 
         if (bool==1) {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           for(m=firstpass; m<=lastpass; m++){      } 
             k2=anint[m][i]+(mint[m][i]/12.);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      fu=(*f)(u); 
               if(agev[m][i]==0) agev[m][i]=agemax+1;      if (fu <= fx) { 
               if(agev[m][i]==1) agev[m][i]=agemax+2;        if (u >= x) a=x; else b=x; 
               if (m<lastpass) {        SHFT(v,w,x,u) 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        SHFT(fv,fw,fx,fu) 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      } else { 
               }        if (u < x) a=u; else b=u; 
                      if (fu <= fw || w == x) { 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          v=w; 
                 dateintsum=dateintsum+k2;          w=u; 
                 k2cpt++;          fv=fw; 
               }          fw=fu; 
             }        } else if (fu <= fv || v == x || v == w) { 
           }          v=u; 
         }          fv=fu; 
       }        } 
              } 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    } 
     nrerror("Too many iterations in brent"); 
       if  (cptcovn>0) {    *xmin=x; 
         fprintf(ficresp, "\n#********** Variable ");    return fx; 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  } 
         fprintf(ficresp, "**********\n#");  
       }  /****************** mnbrak ***********************/
       for(i=1; i<=nlstate;i++)  
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       fprintf(ficresp, "\n");              double (*func)(double)) 
        { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
       for(i=(int)agemin; i <= (int)agemax+3; i++){  the downhill direction (defined by the function as evaluated at the initial points) and returns
         if(i==(int)agemax+3){  new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
           fprintf(ficlog,"Total");  values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
         }else{     */
           if(first==1){    double ulim,u,r,q, dum;
             first=0;    double fu; 
             printf("See log file for details...\n");   
           }    *fa=(*func)(*ax); 
           fprintf(ficlog,"Age %d", i);    *fb=(*func)(*bx); 
         }    if (*fb > *fa) { 
         for(jk=1; jk <=nlstate ; jk++){      SHFT(dum,*ax,*bx,dum) 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      SHFT(dum,*fb,*fa,dum) 
             pp[jk] += freq[jk][m][i];    } 
         }    *cx=(*bx)+GOLD*(*bx-*ax); 
         for(jk=1; jk <=nlstate ; jk++){    *fc=(*func)(*cx); 
           for(m=-1, pos=0; m <=0 ; m++)  #ifdef DEBUG
             pos += freq[jk][m][i];    printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
           if(pp[jk]>=1.e-10){    fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
             if(first==1){  #endif
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
             }      r=(*bx-*ax)*(*fb-*fc); 
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      q=(*bx-*cx)*(*fb-*fa); 
           }else{      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
             if(first==1)        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);      if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
           }        fu=(*func)(u); 
         }  #ifdef DEBUG
         /* f(x)=A(x-u)**2+f(u) */
         for(jk=1; jk <=nlstate ; jk++){        double A, fparabu; 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
             pp[jk] += freq[jk][m][i];        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);
         for(jk=1,pos=0; jk <=nlstate ; jk++)        /* And thus,it can be that fu > *fc even if fparabu < *fc */
           pos += pp[jk];        /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
         for(jk=1; jk <=nlstate ; jk++){          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
           if(pos>=1.e-5){        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
             if(first==1)  #endif 
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  #ifdef MNBRAKORI
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  #else
           }else{        if (fu > *fc) {
             if(first==1)  #ifdef DEBUG
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        printf("mnbrak4  fu > fc \n");
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        fprintf(ficlog, "mnbrak4 fu > fc\n");
           }  #endif
           if( i <= (int) agemax){          /* SHFT(u,*cx,*cx,u) /\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\/  */
             if(pos>=1.e-5){          /* SHFT(*fa,*fc,fu,*fc) /\* (b, u, c) is a bracket while test fb > fc will be fu > fc  will exit *\/ */
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          dum=u; /* Shifting c and u */
               probs[i][jk][j1]= pp[jk]/pos;          u = *cx;
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          *cx = dum;
             }          dum = fu;
             else          fu = *fc;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          *fc =dum;
           }        } else { /* end */
         }  #ifdef DEBUG
                printf("mnbrak3  fu < fc \n");
         for(jk=-1; jk <=nlstate+ndeath; jk++)        fprintf(ficlog, "mnbrak3 fu < fc\n");
           for(m=-1; m <=nlstate+ndeath; m++)  #endif
             if(freq[jk][m][i] !=0 ) {          dum=u; /* Shifting c and u */
             if(first==1)          u = *cx;
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          *cx = dum;
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);          dum = fu;
             }          fu = *fc;
         if(i <= (int) agemax)          *fc =dum;
           fprintf(ficresp,"\n");        }
         if(first==1)  #endif
           printf("Others in log...\n");      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
         fprintf(ficlog,"\n");  #ifdef DEBUG
       }        printf("mnbrak2  u after c but before ulim\n");
     }        fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
   }  #endif
   dateintmean=dateintsum/k2cpt;        fu=(*func)(u); 
          if (fu < *fc) { 
   fclose(ficresp);  #ifdef DEBUG
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        printf("mnbrak2  u after c but before ulim AND fu < fc\n");
   free_vector(pp,1,nlstate);        fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
    #endif
   /* End of Freq */          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 }          SHFT(*fb,*fc,fu,(*func)(u)) 
         } 
 /************ Prevalence ********************/      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
 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)  #ifdef DEBUG
 {  /* Some frequencies */        printf("mnbrak2  u outside ulim (verifying that ulim is beyond c)\n");
          fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  #endif
   double ***freq; /* Frequencies */        u=ulim; 
   double *pp;        fu=(*func)(u); 
   double pos, k2;      } else { /* u could be left to b (if r > q parabola has a maximum) */
   #ifdef DEBUG
   pp=vector(1,nlstate);        printf("mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficlog, "mnbrak2  u could be left to b (if r > q parabola has a maximum)\n");
    #endif
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        u=(*cx)+GOLD*(*cx-*bx); 
   j1=0;        fu=(*func)(u); 
        } /* end tests */
   j=cptcoveff;      SHFT(*ax,*bx,*cx,u) 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      SHFT(*fa,*fb,*fc,fu) 
    #ifdef DEBUG
   for(k1=1; k1<=j;k1++){        printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
     for(i1=1; i1<=ncodemax[k1];i1++){        fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
       j1++;  #endif
          } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
       for (i=-1; i<=nlstate+ndeath; i++)    } 
         for (jk=-1; jk<=nlstate+ndeath; jk++)    
           for(m=agemin; m <= agemax+3; m++)  /*************** linmin ************************/
             freq[i][jk][m]=0;  /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
        resets p to where the function func(p) takes on a minimum along the direction xi from p ,
       for (i=1; i<=imx; i++) {  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
         bool=1;  the value of func at the returned location p . This is actually all accomplished by calling the
         if  (cptcovn>0) {  routines mnbrak and brent .*/
           for (z1=1; z1<=cptcoveff; z1++)  int ncom; 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  double *pcom,*xicom;
               bool=0;  double (*nrfunc)(double []); 
         }   
         if (bool==1) {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
           for(m=firstpass; m<=lastpass; m++){  { 
             k2=anint[m][i]+(mint[m][i]/12.);    double brent(double ax, double bx, double cx, 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {                 double (*f)(double), double tol, double *xmin); 
               if(agev[m][i]==0) agev[m][i]=agemax+1;    double f1dim(double x); 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
               if (m<lastpass) {                double *fc, double (*func)(double)); 
                 if (calagedate>0)    int j; 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    double xx,xmin,bx,ax; 
                 else    double fx,fb,fa;
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];   
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    ncom=n; 
               }    pcom=vector(1,n); 
             }    xicom=vector(1,n); 
           }    nrfunc=func; 
         }    for (j=1;j<=n;j++) { 
       }      pcom[j]=p[j]; 
       for(i=(int)agemin; i <= (int)agemax+3; i++){      xicom[j]=xi[j]; 
         for(jk=1; jk <=nlstate ; jk++){    } 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    ax=0.0; 
             pp[jk] += freq[jk][m][i];    xx=1.0; 
         }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
         for(jk=1; jk <=nlstate ; jk++){    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
           for(m=-1, pos=0; m <=0 ; m++)  #ifdef DEBUG
             pos += freq[jk][m][i];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
          #endif
         for(jk=1; jk <=nlstate ; jk++){    for (j=1;j<=n;j++) { 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      xi[j] *= xmin; 
             pp[jk] += freq[jk][m][i];      p[j] += xi[j]; 
         }    } 
            free_vector(xicom,1,n); 
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    free_vector(pcom,1,n); 
          } 
         for(jk=1; jk <=nlstate ; jk++){      
           if( i <= (int) agemax){  
             if(pos>=1.e-5){  /*************** powell ************************/
               probs[i][jk][j1]= 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-
         }/* end jk */  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
       }/* end i */  such that failure to decrease by more than this amount on one iteration signals doneness. On
     } /* end i1 */  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
   } /* end k1 */  function value at p , and iter is the number of iterations taken. The routine linmin is used.
    */
    void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);              double (*func)(double [])) 
   free_vector(pp,1,nlstate);  { 
      void linmin(double p[], double xi[], int n, double *fret, 
 }  /* End of Freq */                double (*func)(double [])); 
     int i,ibig,j; 
 /************* Waves Concatenation ***************/    double del,t,*pt,*ptt,*xit;
     double directest;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    double fp,fptt;
 {    double *xits;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    int niterf, itmp;
      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    pt=vector(1,n); 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    ptt=vector(1,n); 
      and mw[mi+1][i]. dh depends on stepm.    xit=vector(1,n); 
      */    xits=vector(1,n); 
     *fret=(*func)(p); 
   int i, mi, m;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      rcurr_time = time(NULL);  
      double sum=0., jmean=0.;*/    for (*iter=1;;++(*iter)) { 
   int first;      fp=(*fret); 
   int j, k=0,jk, ju, jl;      ibig=0; 
   double sum=0.;      del=0.0; 
   first=0;      rlast_time=rcurr_time;
   jmin=1e+5;      /* (void) gettimeofday(&curr_time,&tzp); */
   jmax=-1;      rcurr_time = time(NULL);  
   jmean=0.;      curr_time = *localtime(&rcurr_time);
   for(i=1; i<=imx; i++){      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
     mi=0;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
     m=firstpass;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
     while(s[m][i] <= nlstate){     for (i=1;i<=n;i++) {
       if(s[m][i]>=1)        printf(" %d %.12f",i, p[i]);
         mw[++mi][i]=m;        fprintf(ficlog," %d %.12lf",i, p[i]);
       if(m >=lastpass)        fprintf(ficrespow," %.12lf", p[i]);
         break;      }
       else      printf("\n");
         m++;      fprintf(ficlog,"\n");
     }/* end while */      fprintf(ficrespow,"\n");fflush(ficrespow);
     if (s[m][i] > nlstate){      if(*iter <=3){
       mi++;     /* Death is another wave */        tml = *localtime(&rcurr_time);
       /* if(mi==0)  never been interviewed correctly before death */        strcpy(strcurr,asctime(&tml));
          /* Only death is a correct wave */        rforecast_time=rcurr_time; 
       mw[mi][i]=m;        itmp = strlen(strcurr);
     }        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           strcurr[itmp-1]='\0';
     wav[i]=mi;        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
     if(mi==0){        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       if(first==0){        for(niterf=10;niterf<=30;niterf+=10){
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         first=1;          forecast_time = *localtime(&rforecast_time);
       }          strcpy(strfor,asctime(&forecast_time));
       if(first==1){          itmp = strlen(strfor);
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);          if(strfor[itmp-1]=='\n')
       }          strfor[itmp-1]='\0';
     } /* end mi==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);
   }          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
         }
   for(i=1; i<=imx; i++){      }
     for(mi=1; mi<wav[i];mi++){      for (i=1;i<=n;i++) { 
       if (stepm <=0)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         dh[mi][i]=1;        fptt=(*fret); 
       else{  #ifdef DEBUG
         if (s[mw[mi+1][i]][i] > nlstate) {            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
           if (agedc[i] < 2*AGESUP) {            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  #endif
           if(j==0) j=1;  /* Survives at least one month after exam */        printf("%d",i);fflush(stdout);
           k=k+1;        fprintf(ficlog,"%d",i);fflush(ficlog);
           if (j >= jmax) jmax=j;        linmin(p,xit,n,fret,func); /* xit[n] has been loaded for direction i */
           if (j <= jmin) jmin=j;        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions 
           sum=sum+j;                                         because that direction will be replaced unless the gain del is small
           /*if (j<0) printf("j=%d num=%d \n",j,i); */                                        in comparison with the 'probable' gain, mu^2, with the last average direction.
           }                                        Unless the n directions are conjugate some gain in the determinant may be obtained
         }                                        with the new direction.
         else{                                        */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          del=fabs(fptt-(*fret)); 
           k=k+1;          ibig=i; 
           if (j >= jmax) jmax=j;        } 
           else if (j <= jmin)jmin=j;  #ifdef DEBUG
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        printf("%d %.12e",i,(*fret));
           sum=sum+j;        fprintf(ficlog,"%d %.12e",i,(*fret));
         }        for (j=1;j<=n;j++) {
         jk= j/stepm;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         jl= j -jk*stepm;          printf(" x(%d)=%.12e",j,xit[j]);
         ju= j -(jk+1)*stepm;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         if(jl <= -ju)        }
           dh[mi][i]=jk;        for(j=1;j<=n;j++) {
         else          printf(" p(%d)=%.12e",j,p[j]);
           dh[mi][i]=jk+1;          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
         if(dh[mi][i]==0)        }
           dh[mi][i]=1; /* At least one step */        printf("\n");
       }        fprintf(ficlog,"\n");
     }  #endif
   }      } /* end i */
   jmean=sum/k;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  #ifdef DEBUG
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        int k[2],l;
  }        k[0]=1;
         k[1]=-1;
 /*********** Tricode ****************************/        printf("Max: %.12e",(*func)(p));
 void tricode(int *Tvar, int **nbcode, int imx)        fprintf(ficlog,"Max: %.12e",(*func)(p));
 {        for (j=1;j<=n;j++) {
   int Ndum[20],ij=1, k, j, i;          printf(" %.12e",p[j]);
   int cptcode=0;          fprintf(ficlog," %.12e",p[j]);
   cptcoveff=0;        }
          printf("\n");
   for (k=0; k<19; k++) Ndum[k]=0;        fprintf(ficlog,"\n");
   for (k=1; k<=7; k++) ncodemax[k]=0;        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     for (i=1; i<=imx; i++) {            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       ij=(int)(covar[Tvar[j]][i]);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       Ndum[ij]++;          }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       if (ij > cptcode) cptcode=ij;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     }        }
   #endif
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;  
     }        free_vector(xit,1,n); 
     ij=1;        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
     for (i=1; i<=ncodemax[j]; i++) {        return; 
       for (k=0; k<=19; k++) {      } 
         if (Ndum[k] != 0) {      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
           nbcode[Tvar[j]][ij]=k;      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
                  ptt[j]=2.0*p[j]-pt[j]; 
           ij++;        xit[j]=p[j]-pt[j]; 
         }        pt[j]=p[j]; 
         if (ij > ncodemax[j]) break;      } 
       }        fptt=(*func)(ptt); /* f_3 */
     }      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
   }          /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
         /* From x1 (P0) distance of x2 is at h and x3 is 2h */
  for (k=0; k<19; k++) Ndum[k]=0;        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
         /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
  for (i=1; i<=ncovmodel-2; i++) {        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
    ij=Tvar[i];        /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
    Ndum[ij]++;        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
  }  #ifdef NRCORIGINAL
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
  ij=1;  #else
  for (i=1; i<=10; i++) {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
    if((Ndum[i]!=0) && (i<=ncovcol)){        t= t- del*SQR(fp-fptt);
      Tvaraff[ij]=i;  #endif
      ij++;        directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
    }  #ifdef DEBUG
  }        printf("t1= %.12lf, t2= %.12lf, t=%.12lf  directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
          fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
  cptcoveff=ij-1;        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));
         fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
 /*********** Health Expectancies ****************/               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
 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 )        fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
   #endif
 {  #ifdef POWELLORIGINAL
   /* Health expectancies */        if (t < 0.0) { /* Then we use it for new direction */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  #else
   double age, agelim, hf;        if (directest*t < 0.0) { /* Contradiction between both tests */
   double ***p3mat,***varhe;        printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt);
   double **dnewm,**doldm;        printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
   double *xp;        fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt);
   double **gp, **gm;        fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
   double ***gradg, ***trgradg;      } 
   int theta;        if (directest < 0.0) { /* Then we use it for new direction */
   #endif
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction.*/
   xp=vector(1,npar);          for (j=1;j<=n;j++) { 
   dnewm=matrix(1,nlstate*2,1,npar);            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
   doldm=matrix(1,nlstate*2,1,nlstate*2);            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
            }
   fprintf(ficreseij,"# Health expectancies\n");          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   fprintf(ficreseij,"# Age");          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)  #ifdef DEBUG
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   fprintf(ficreseij,"\n");          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
   if(estepm < stepm){            printf(" %.12e",xit[j]);
     printf ("Problem %d lower than %d\n",estepm, stepm);            fprintf(ficlog," %.12e",xit[j]);
   }          }
   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  #endif
    * if stepm=24 months pijx are given only every 2 years and by summing them        } /* end of t negative */
    * we are calculating an estimate of the Life Expectancy assuming a linear      } /* end if (fptt < fp)  */
    * progression inbetween and thus overestimating or underestimating according    } 
    * to the curvature of the survival function. If, for the same date, we  } 
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  
    * to compare the new estimate of Life expectancy with the same linear  /**** Prevalence limit (stable or period prevalence)  ****************/
    * hypothesis. A more precise result, taking into account a more precise  
    * curvature will be obtained if estepm is as small as stepm. */  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   {
   /* For example we decided to compute the life expectancy with the smallest unit */    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.       matrix by transitions matrix until convergence is reached */
      nhstepm is the number of hstepm from age to agelim    
      nstepm is the number of stepm from age to agelin.    int i, ii,j,k;
      Look at hpijx to understand the reason of that which relies in memory size    double min, max, maxmin, maxmax,sumnew=0.;
      and note for a fixed period like estepm months */    /* double **matprod2(); */ /* test */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    double **out, cov[NCOVMAX+1], **pmij();
      survival function given by stepm (the optimization length). Unfortunately it    double **newm;
      means that if the survival funtion is printed only each two years of age and if    double agefin, delaymax=50 ; /* Max number of years to converge */
      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.    for (ii=1;ii<=nlstate+ndeath;ii++)
   */      for (j=1;j<=nlstate+ndeath;j++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
   agelim=AGESUP;    
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    cov[1]=1.;
     /* nhstepm age range expressed in number of stepm */    
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     /* if (stepm >= YEARM) hstepm=1;*/      newm=savm;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      /* Covariates have to be included here again */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      cov[2]=agefin;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);      
     gp=matrix(0,nhstepm,1,nlstate*2);      for (k=1; k<=cptcovn;k++) {
     gm=matrix(0,nhstepm,1,nlstate*2);        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         /*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]]);*/
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        /* 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]]]; */
       
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     /* Computing Variances of health expectancies */      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
      for(theta=1; theta <=npar; theta++){      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
       for(i=1; i<=npar; i++){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      
       }      savm=oldm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        oldm=newm;
        maxmax=0.;
       cptj=0;      for(j=1;j<=nlstate;j++){
       for(j=1; j<= nlstate; j++){        min=1.;
         for(i=1; i<=nlstate; i++){        max=0.;
           cptj=cptj+1;        for(i=1; i<=nlstate; i++) {
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){          sumnew=0;
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+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);*/
       }          max=FMAX(max,prlim[i][j]);
                min=FMIN(min,prlim[i][j]);
              }
       for(i=1; i<=npar; i++)        maxmin=max-min;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        maxmax=FMAX(maxmax,maxmin);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        } /* j loop */
            if(maxmax < ftolpl){
       cptj=0;        return prlim;
       for(j=1; j<= nlstate; j++){      }
         for(i=1;i<=nlstate;i++){    } /* age loop */
           cptj=cptj+1;    return prlim; /* should not reach here */
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){  }
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }  /*************** transition probabilities ***************/ 
         }  
       }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       for(j=1; j<= nlstate*2; j++)  {
         for(h=0; h<=nhstepm-1; h++){    /* According to parameters values stored in x and the covariate's values stored in cov,
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];       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
 /* End theta */       ncth covariate in the global vector x is given by the formula:
        j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
        Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
      for(h=0; h<=nhstepm-1; h++)       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
       for(j=1; j<=nlstate*2;j++)       Outputs ps[i][j] the probability to be observed in j being in j according to
         for(theta=1; theta <=npar; theta++)       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
           trgradg[h][j][theta]=gradg[h][theta][j];    */
          double s1, lnpijopii;
     /*double t34;*/
      for(i=1;i<=nlstate*2;i++)    int i,j, nc, ii, jj;
       for(j=1;j<=nlstate*2;j++)  
         varhe[i][j][(int)age] =0.;      for(i=1; i<= nlstate; i++){
         for(j=1; j<i;j++){
      printf("%d|",(int)age);fflush(stdout);          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);            /*lnpijopii += param[i][j][nc]*cov[nc];*/
      for(h=0;h<=nhstepm-1;h++){            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
       for(k=0;k<=nhstepm-1;k++){  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);          }
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         for(i=1;i<=nlstate*2;i++)  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
           for(j=1;j<=nlstate*2;j++)        }
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;        for(j=i+1; j<=nlstate+ndeath;j++){
       }          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     }            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
     /* Computing expectancies */            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
     for(i=1; i<=nlstate;i++)  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
       for(j=1; j<=nlstate;j++)          }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        }
                }
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/      
       for(i=1; i<= nlstate; i++){
         }        s1=0;
         for(j=1; j<i; j++){
     fprintf(ficreseij,"%3.0f",age );          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
     cptj=0;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
     for(i=1; i<=nlstate;i++)        }
       for(j=1; j<=nlstate;j++){        for(j=i+1; j<=nlstate+ndeath; j++){
         cptj++;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       }        }
     fprintf(ficreseij,"\n");        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
            ps[i][i]=1./(s1+1.);
     free_matrix(gm,0,nhstepm,1,nlstate*2);        /* Computing other pijs */
     free_matrix(gp,0,nhstepm,1,nlstate*2);        for(j=1; j<i; j++)
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);          ps[i][j]= exp(ps[i][j])*ps[i][i];
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);        for(j=i+1; j<=nlstate+ndeath; j++)
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   printf("\n");      } /* end i */
   fprintf(ficlog,"\n");      
       for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   free_vector(xp,1,npar);        for(jj=1; jj<= nlstate+ndeath; jj++){
   free_matrix(dnewm,1,nlstate*2,1,npar);          ps[ii][jj]=0;
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);          ps[ii][ii]=1;
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);        }
 }      }
       
 /************ Variance ******************/      
 void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased)      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
 {      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   /* Variance of health expectancies */      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      /*   } */
   /* double **newm;*/      /*   printf("\n "); */
   double **dnewm,**doldm;      /* } */
   double **dnewmp,**doldmp;      /* printf("\n ");printf("%lf ",cov[2]);*/
   int i, j, nhstepm, hstepm, h, nstepm ;      /*
   int k, cptcode;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   double *xp;        goto end;*/
   double **gp, **gm;  /* for var eij */      return ps;
   double ***gradg, ***trgradg; /*for var eij */  }
   double **gradgp, **trgradgp; /* for var p point j */  
   double *gpp, *gmp; /* for var p point j */  /**************** Product of 2 matrices ******************/
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */  
   double ***p3mat;  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   double age,agelim, hf;  {
   int theta;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   char digit[4];       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   char digitp[16];    /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
   char fileresprobmorprev[FILENAMELENGTH];       a pointer to pointers identical to out */
     int i, j, k;
   if(popbased==1)    for(i=nrl; i<= nrh; i++)
     strcpy(digitp,"-populbased-");      for(k=ncolol; k<=ncoloh; k++){
   else        out[i][k]=0.;
     strcpy(digitp,"-stablbased-");        for(j=ncl; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
   strcpy(fileresprobmorprev,"prmorprev");      }
   sprintf(digit,"%-d",ij);    return out;
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/  }
   strcat(fileresprobmorprev,digit); /* Tvar to be done */  
   strcat(fileresprobmorprev,digitp); /* Popbased or not */  
   strcat(fileresprobmorprev,fileres);  /************* Higher Matrix Product ***************/
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobmorprev);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);  {
   }    /* Computes the transition matrix starting at age 'age' over 
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);       'nhstepm*hstepm*stepm' months (i.e. until
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");       nhstepm*hstepm matrices. 
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){       (typically every 2 years instead of every month which is too big 
     fprintf(ficresprobmorprev," p.%-d SE",j);       for the memory).
     for(i=1; i<=nlstate;i++)       Model is determined by parameters x and covariates have to be 
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);       included manually here. 
   }    
   fprintf(ficresprobmorprev,"\n");       */
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {  
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    int i, j, d, h, k;
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    double **out, cov[NCOVMAX+1];
     exit(0);    double **newm;
   }  
   else{    /* Hstepm could be zero and should return the unit matrix */
     fprintf(ficgp,"\n# Routine varevsij");    for (i=1;i<=nlstate+ndeath;i++)
   }      for (j=1;j<=nlstate+ndeath;j++){
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {        oldm[i][j]=(i==j ? 1.0 : 0.0);
     printf("Problem with html file: %s\n", optionfilehtm);        po[i][j][0]=(i==j ? 1.0 : 0.0);
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);      }
     exit(0);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   }    for(h=1; h <=nhstepm; h++){
   else{      for(d=1; d <=hstepm; d++){
     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");        newm=savm;
   }        /* Covariates have to be included here again */
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   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");        for (k=1; k<=cptcovn;k++) 
   fprintf(ficresvij,"# Age");          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   for(i=1; i<=nlstate;i++)        for (k=1; k<=cptcovage;k++)
     for(j=1; j<=nlstate;j++)          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   fprintf(ficresvij,"\n");          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   doldm=matrix(1,nlstate,1,nlstate);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);        oldm=newm;
   gpp=vector(nlstate+1,nlstate+ndeath);      }
   gmp=vector(nlstate+1,nlstate+ndeath);      for(i=1; i<=nlstate+ndeath; i++)
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/        for(j=1;j<=nlstate+ndeath;j++) {
            po[i][j][h]=newm[i][j];
   if(estepm < stepm){          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
     printf ("Problem %d lower than %d\n",estepm, stepm);        }
   }      /*printf("h=%d ",h);*/
   else  hstepm=estepm;      } /* end h */
   /* For example we decided to compute the life expectancy with the smallest unit */  /*     printf("\n H=%d \n",h); */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    return po;
      nhstepm is the number of hstepm from age to agelim  }
      nstepm is the number of stepm from age to agelin.  
      Look at hpijx to understand the reason of that which relies in memory size  #ifdef NLOPT
      and note for a fixed period like k years */    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    double fret;
      survival function given by stepm (the optimization length). Unfortunately it    double *xt;
      means that if the survival funtion is printed only each two years of age and if    int j;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    myfunc_data *d2 = (myfunc_data *) pd;
      results. So we changed our mind and took the option of the best precision.  /* xt = (p1-1); */
   */    xt=vector(1,n); 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    printf("Function = %.12lf ",fret);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    printf("\n");
     gp=matrix(0,nhstepm,1,nlstate);   free_vector(xt,1,n);
     gm=matrix(0,nhstepm,1,nlstate);    return fret;
   }
   #endif
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */  /*************** log-likelihood *************/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  double func( double *x)
       }  {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int i, ii, j, k, mi, d, kk;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     double **out;
       if (popbased==1) {    double sw; /* Sum of weights */
         for(i=1; i<=nlstate;i++)    double lli; /* Individual log likelihood */
           prlim[i][i]=probs[(int)age][i][ij];    int s1, s2;
       }    double bbh, survp;
      long ipmx;
       for(j=1; j<= nlstate; j++){    /*extern weight */
         for(h=0; h<=nhstepm; h++){    /* We are differentiating ll according to initial status */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    /*for(i=1;i<imx;i++) 
         }      printf(" %d\n",s[4][i]);
       }    */
       /* This for computing forces of mortality (h=1)as a weighted average */  
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){    ++countcallfunc;
         for(i=1; i<= nlstate; i++)  
           gpp[j] += prlim[i][i]*p3mat[i][j][1];    cov[1]=1.;
       }      
       /* end force of mortality */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
       for(i=1; i<=npar; i++) /* Computes gradient */    if(mle==1){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          /* Computes the values of the ncovmodel covariates of the model
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
             Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
       if (popbased==1) {           to be observed in j being in i according to the model.
         for(i=1; i<=nlstate;i++)         */
           prlim[i][i]=probs[(int)age][i][ij];        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
       }          cov[2+k]=covar[Tvar[k]][i];
         }
       for(j=1; j<= nlstate; j++){        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
         for(h=0; h<=nhstepm; h++){           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)           has been calculated etc */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
       /* This for computing force of mortality (h=1)as a weighted average */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(i=1; i<= nlstate; i++)            }
           gmp[j] += prlim[i][i]*p3mat[i][j][1];          for(d=0; d<dh[mi][i]; d++){
       }                newm=savm;
       /* end force of mortality */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
       for(j=1; j<= nlstate; j++) /* vareij */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
         for(h=0; h<=nhstepm; h++){            }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            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++){ /* var mu */            savm=oldm;
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];            oldm=newm;
       }          } /* end mult */
         
     } /* End theta */          /*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.
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */           * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
     for(h=0; h<=nhstepm; h++) /* veij */           * the nearest (and in case of equal distance, to the lowest) interval but now
       for(j=1; j<=nlstate;j++)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         for(theta=1; theta <=npar; theta++)           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           trgradg[h][j][theta]=gradg[h][theta][j];           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */           * -stepm/2 to stepm/2 .
       for(theta=1; theta <=npar; theta++)           * For stepm=1 the results are the same as for previous versions of Imach.
         trgradgp[j][theta]=gradgp[theta][j];           * For stepm > 1 the results are less biased than in previous versions. 
            */
     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.;          /* bias bh is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
     for(h=0;h<=nhstepm;h++){           */
       for(k=0;k<=nhstepm;k++){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          if( s2 > nlstate){ 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            /* i.e. if s2 is a death state and if the date of death is known 
         for(i=1;i<=nlstate;i++)               then the contribution to the likelihood is the probability to 
           for(j=1;j<=nlstate;j++)               die between last step unit time and current  step unit time, 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;               which is also equal to probability to die before dh 
       }               minus probability to die before dh-stepm . 
     }               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
     /* pptj */          health state: the date of the interview describes the actual state
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);          and not the date of a change in health state. The former idea was
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);          to consider that at each interview the state was recorded
     for(j=nlstate+1;j<=nlstate+ndeath;j++)          (healthy, disable or death) and IMaCh was corrected; but when we
       for(i=nlstate+1;i<=nlstate+ndeath;i++)          introduced the exact date of death then we should have modified
         varppt[j][i]=doldmp[j][i];          the contribution of an exact death to the likelihood. This new
     /* end ppptj */          contribution is smaller and very dependent of the step unit
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);            stepm. It is no more the probability to die between last interview
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);          and month of death but the probability to survive from last
            interview up to one month before death multiplied by the
     if (popbased==1) {          probability to die within a month. Thanks to Chris
       for(i=1; i<=nlstate;i++)          Jackson for correcting this bug.  Former versions increased
         prlim[i][i]=probs[(int)age][i][ij];          mortality artificially. The bad side is that we add another loop
     }          which slows down the processing. The difference can be up to 10%
              lower mortality.
     /* This for computing force of mortality (h=1)as a weighted average */            */
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){          /* If, at the beginning of the maximization mostly, the
       for(i=1; i<= nlstate; i++)             cumulative probability or probability to be dead is
         gmp[j] += prlim[i][i]*p3mat[i][j][1];             constant (ie = 1) over time d, the difference is equal to
     }                 0.  out[s1][3] = savm[s1][3]: probability, being at state
     /* end force of mortality */             s1 at precedent wave, to be dead a month before current
              wave is equal to probability, being at state s1 at
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);             precedent wave, to be dead at mont of the current
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){             wave. Then the observed probability (that this person died)
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));             is null according to current estimated parameter. In fact,
       for(i=1; i<=nlstate;i++){             it should be very low but not zero otherwise the log go to
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);             infinity.
       }          */
     }  /* #ifdef INFINITYORIGINAL */
     fprintf(ficresprobmorprev,"\n");  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
   /* #else */
     fprintf(ficresvij,"%.0f ",age );  /*        if ((out[s1][s2] - savm[s1][s2]) < mytinydouble)  */
     for(i=1; i<=nlstate;i++)  /*          lli=log(mytinydouble); */
       for(j=1; j<=nlstate;j++){  /*        else */
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
       }  /* #endif */
     fprintf(ficresvij,"\n");              lli=log(out[s1][s2] - savm[s1][s2]);
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);          } else if  (s2==-2) {
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            for (j=1,survp=0. ; j<=nlstate; j++) 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            /*survp += out[s1][j]; */
   } /* End age */            lli= log(survp);
   free_vector(gpp,nlstate+1,nlstate+ndeath);          }
   free_vector(gmp,nlstate+1,nlstate+ndeath);          
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);          else if  (s2==-4) { 
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/            for (j=3,survp=0. ; j<=nlstate; j++)  
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */            lli= log(survp); 
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");          } 
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);  
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);          else if  (s2==-5) { 
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);            for (j=1,survp=0. ; j<=2; j++)  
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   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);            lli= log(survp); 
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);          } 
           
   free_vector(xp,1,npar);          else{
   free_matrix(doldm,1,nlstate,1,nlstate);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   free_matrix(dnewm,1,nlstate,1,npar);            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);          } 
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);          /*if(lli ==000.0)*/
   fclose(ficresprobmorprev);          /*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); */
   fclose(ficgp);          ipmx +=1;
   fclose(fichtm);          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 }          /* if (lli < log(mytinydouble)){ */
           /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
 /************ Variance of prevlim ******************/          /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          /* } */
 {        } /* end of wave */
   /* Variance of prevalence limit */      } /* end of individual */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    }  else if(mle==2){
   double **newm;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double **dnewm,**doldm;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int i, j, nhstepm, hstepm;        for(mi=1; mi<= wav[i]-1; mi++){
   int k, cptcode;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double *xp;            for (j=1;j<=nlstate+ndeath;j++){
   double *gp, *gm;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **gradg, **trgradg;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double age,agelim;            }
   int theta;          for(d=0; d<=dh[mi][i]; d++){
                newm=savm;
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficresvpl,"# Age");            for (kk=1; kk<=cptcovage;kk++) {
   for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       fprintf(ficresvpl," %1d-%1d",i,i);            }
   fprintf(ficresvpl,"\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   xp=vector(1,npar);            savm=oldm;
   dnewm=matrix(1,nlstate,1,npar);            oldm=newm;
   doldm=matrix(1,nlstate,1,nlstate);          } /* end mult */
          
   hstepm=1*YEARM; /* Every year of age */          s1=s[mw[mi][i]][i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          s2=s[mw[mi+1][i]][i];
   agelim = AGESUP;          bbh=(double)bh[mi][i]/(double)stepm; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          ipmx +=1;
     if (stepm >= YEARM) hstepm=1;          sw += weight[i];
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     gradg=matrix(1,npar,1,nlstate);        } /* end of wave */
     gp=vector(1,nlstate);      } /* end of individual */
     gm=vector(1,nlstate);    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(theta=1; theta <=npar; theta++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(mi=1; mi<= wav[i]-1; mi++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1;i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         gp[i] = prlim[i][i];            }
              for(d=0; d<dh[mi][i]; d++){
       for(i=1; i<=npar; i++) /* Computes gradient */            newm=savm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            for (kk=1; kk<=cptcovage;kk++) {
       for(i=1;i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         gm[i] = prlim[i][i];            }
             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));
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            savm=oldm;
     } /* End theta */            oldm=newm;
           } /* end mult */
     trgradg =matrix(1,nlstate,1,npar);        
           s1=s[mw[mi][i]][i];
     for(j=1; j<=nlstate;j++)          s2=s[mw[mi+1][i]][i];
       for(theta=1; theta <=npar; theta++)          bbh=(double)bh[mi][i]/(double)stepm; 
         trgradg[j][theta]=gradg[theta][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])); /* exponential inter-extrapolation */
           ipmx +=1;
     for(i=1;i<=nlstate;i++)          sw += weight[i];
       varpl[i][(int)age] =0.;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        } /* end of wave */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      } /* end of individual */
     for(i=1;i<=nlstate;i++)    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fprintf(ficresvpl,"%.0f ",age );        for(mi=1; mi<= wav[i]-1; mi++){
     for(i=1; i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            for (j=1;j<=nlstate+ndeath;j++){
     fprintf(ficresvpl,"\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_vector(gp,1,nlstate);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_vector(gm,1,nlstate);            }
     free_matrix(gradg,1,npar,1,nlstate);          for(d=0; d<dh[mi][i]; d++){
     free_matrix(trgradg,1,nlstate,1,npar);            newm=savm;
   } /* End age */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   free_vector(xp,1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_matrix(doldm,1,nlstate,1,npar);            }
   free_matrix(dnewm,1,nlstate,1,nlstate);          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
 /************ Variance of one-step probabilities  ******************/            oldm=newm;
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          } /* end mult */
 {        
   int i, j=0,  i1, k1, l1, t, tj;          s1=s[mw[mi][i]][i];
   int k2, l2, j1,  z1;          s2=s[mw[mi+1][i]][i];
   int k=0,l, cptcode;          if( s2 > nlstate){ 
   int first=1, first1;            lli=log(out[s1][s2] - savm[s1][s2]);
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;          }else{
   double **dnewm,**doldm;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   double *xp;          }
   double *gp, *gm;          ipmx +=1;
   double **gradg, **trgradg;          sw += weight[i];
   double **mu;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double age,agelim, cov[NCOVMAX];  /*      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]); */
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */        } /* end of wave */
   int theta;      } /* end of individual */
   char fileresprob[FILENAMELENGTH];    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   char fileresprobcov[FILENAMELENGTH];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   char fileresprobcor[FILENAMELENGTH];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   double ***varpij;          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   strcpy(fileresprob,"prob");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcat(fileresprob,fileres);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            }
     printf("Problem with resultfile: %s\n", fileresprob);          for(d=0; d<dh[mi][i]; d++){
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   strcpy(fileresprobcov,"probcov");            for (kk=1; kk<=cptcovage;kk++) {
   strcat(fileresprobcov,fileres);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {            }
     printf("Problem with resultfile: %s\n", fileresprobcov);          
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   strcpy(fileresprobcor,"probcor");            savm=oldm;
   strcat(fileresprobcor,fileres);            oldm=newm;
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {          } /* end mult */
     printf("Problem with resultfile: %s\n", fileresprobcor);        
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);          ipmx +=1;
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);          sw += weight[i];
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);          /*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(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);        } /* end of wave */
        } /* end of individual */
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    } /* End of if */
   fprintf(ficresprob,"# Age");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   fprintf(ficresprobcov,"# Age");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    return -l;
   fprintf(ficresprobcov,"# Age");  }
   
   /*************** log-likelihood *************/
   for(i=1; i<=nlstate;i++)  double funcone( double *x)
     for(j=1; j<=(nlstate+ndeath);j++){  {
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    /* Same as likeli but slower because of a lot of printf and if */
       fprintf(ficresprobcov," p%1d-%1d ",i,j);    int i, ii, j, k, mi, d, kk;
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     }      double **out;
   fprintf(ficresprob,"\n");    double lli; /* Individual log likelihood */
   fprintf(ficresprobcov,"\n");    double llt;
   fprintf(ficresprobcor,"\n");    int s1, s2;
   xp=vector(1,npar);    double bbh, survp;
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    /*extern weight */
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));    /* We are differentiating ll according to initial status */
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);    /*for(i=1;i<imx;i++) 
   first=1;      printf(" %d\n",s[4][i]);
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    */
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    cov[1]=1.;
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);  
     exit(0);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   }  
   else{    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fprintf(ficgp,"\n# Routine varprob");      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }      for(mi=1; mi<= wav[i]-1; mi++){
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {        for (ii=1;ii<=nlstate+ndeath;ii++)
     printf("Problem with html file: %s\n", optionfilehtm);          for (j=1;j<=nlstate+ndeath;j++){
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     exit(0);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }          }
   else{        for(d=0; d<dh[mi][i]; d++){
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");          newm=savm;
     fprintf(fichtm,"\n");          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     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");          }
     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");          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
            /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
   cov[1]=1;          savm=oldm;
   tj=cptcoveff;          oldm=newm;
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}        } /* end mult */
   j1=0;        
   for(t=1; t<=tj;t++){        s1=s[mw[mi][i]][i];
     for(i1=1; i1<=ncodemax[t];i1++){        s2=s[mw[mi+1][i]][i];
       j1++;        bbh=(double)bh[mi][i]/(double)stepm; 
              /* bias is positive if real duration
       if  (cptcovn>0) {         * is higher than the multiple of stepm and negative otherwise.
         fprintf(ficresprob, "\n#********** Variable ");         */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         fprintf(ficresprob, "**********\n#");          lli=log(out[s1][s2] - savm[s1][s2]);
         fprintf(ficresprobcov, "\n#********** Variable ");        } else if  (s2==-2) {
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (j=1,survp=0. ; j<=nlstate; j++) 
         fprintf(ficresprobcov, "**********\n#");            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                  lli= log(survp);
         fprintf(ficgp, "\n#********** Variable ");        }else if (mle==1){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         fprintf(ficgp, "**********\n#");        } else if(mle==2){
                  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
                } else if(mle==3){  /* exponential inter-extrapolation */
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");          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 (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");          lli=log(out[s1][s2]); /* Original formula */
                } else{  /* mle=0 back to 1 */
         fprintf(ficresprobcor, "\n#********** Variable ");              lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          /*lli=log(out[s1][s2]); */ /* Original formula */
         fprintf(ficgp, "**********\n#");            } /* End of if */
       }        ipmx +=1;
              sw += weight[i];
       for (age=bage; age<=fage; age ++){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         cov[2]=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]); */
         for (k=1; k<=cptcovn;k++) {        if(globpr){
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
         }   %11.6f %11.6f %11.6f ", \
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
         for (k=1; k<=cptcovprod;k++)                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                    llt +=ll[k]*gipmx/gsw;
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);          }
         gp=vector(1,(nlstate)*(nlstate+ndeath));          fprintf(ficresilk," %10.6f\n", -llt);
         gm=vector(1,(nlstate)*(nlstate+ndeath));        }
          } /* end of wave */
         for(theta=1; theta <=npar; theta++){    } /* end of individual */
           for(i=1; i<=npar; i++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
              l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    if(globpr==0){ /* First time we count the contributions and weights */
                gipmx=ipmx;
           k=0;      gsw=sw;
           for(i=1; i<= (nlstate); i++){    }
             for(j=1; j<=(nlstate+ndeath);j++){    return -l;
               k=k+1;  }
               gp[k]=pmmij[i][j];  
             }  
           }  /*************** function likelione ***********/
            void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
           for(i=1; i<=npar; i++)  {
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    /* This routine should help understanding what is done with 
           the selection of individuals/waves and
           pmij(pmmij,cov,ncovmodel,xp,nlstate);       to check the exact contribution to the likelihood.
           k=0;       Plotting could be done.
           for(i=1; i<=(nlstate); i++){     */
             for(j=1; j<=(nlstate+ndeath);j++){    int k;
               k=k+1;  
               gm[k]=pmmij[i][j];    if(*globpri !=0){ /* Just counts and sums, no printings */
             }      strcpy(fileresilk,"ilk"); 
           }      strcat(fileresilk,fileres);
            if((ficresilk=fopen(fileresilk,"w"))==NULL) {
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)        printf("Problem with resultfile: %s\n", fileresilk);
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         }      }
       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");
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
           for(theta=1; theta <=npar; theta++)      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
             trgradg[j][theta]=gradg[theta][j];      for(k=1; k<=nlstate; k++) 
                fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);    }
          
         pmij(pmmij,cov,ncovmodel,x,nlstate);    *fretone=(*funcone)(p);
            if(*globpri !=0){
         k=0;      fclose(ficresilk);
         for(i=1; i<=(nlstate); i++){      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
           for(j=1; j<=(nlstate+ndeath);j++){      fflush(fichtm); 
             k=k+1;    } 
             mu[k][(int) age]=pmmij[i][j];    return;
           }  }
         }  
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)  
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)  /*********** Maximum Likelihood Estimation ***************/
             varpij[i][j][(int)age] = doldm[i][j];  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         /*printf("\n%d ",(int)age);  {
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    int i,j, iter=0;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    double **xi;
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    double fret;
      }*/    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
         fprintf(ficresprob,"\n%d ",(int)age);  
         fprintf(ficresprobcov,"\n%d ",(int)age);  #ifdef NLOPT
         fprintf(ficresprobcor,"\n%d ",(int)age);    int creturn;
     nlopt_opt opt;
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));    double *lb;
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    double minf; /* the minimum objective value, upon return */
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);    double * p1; /* Shifted parameters from 0 instead of 1 */
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);    myfunc_data dinst, *d = &dinst;
         }  #endif
         i=0;  
         for (k=1; k<=(nlstate);k++){  
           for (l=1; l<=(nlstate+ndeath);l++){    xi=matrix(1,npar,1,npar);
             i=i++;    for (i=1;i<=npar;i++)
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);      for (j=1;j<=npar;j++)
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);        xi[i][j]=(i==j ? 1.0 : 0.0);
             for (j=1; j<=i;j++){    printf("Powell\n");  fprintf(ficlog,"Powell\n");
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);    strcpy(filerespow,"pow"); 
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));    strcat(filerespow,fileres);
             }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
           }      printf("Problem with resultfile: %s\n", filerespow);
         }/* end of loop for state */      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       } /* end of loop for age */    }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /* Confidence intervalle of pij  */    for (i=1;i<=nlstate;i++)
       /*      for(j=1;j<=nlstate+ndeath;j++)
       fprintf(ficgp,"\nset noparametric;unset label");        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");    fprintf(ficrespow,"\n");
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");  #ifdef POWELL
       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);    powell(p,xi,npar,ftol,&iter,&fret,func);
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);  #endif
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);  
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);  #ifdef NLOPT
       */  #ifdef NEWUOA
     opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/  #else
       first1=1;    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
       for (k1=1; k1<=(nlstate);k1++){  #endif
         for (l1=1; l1<=(nlstate+ndeath);l1++){    lb=vector(0,npar-1);
           if(l1==k1) continue;    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
           i=(k1-1)*(nlstate+ndeath)+l1;    nlopt_set_lower_bounds(opt, lb);
           for (k2=1; k2<=(nlstate);k2++){    nlopt_set_initial_step1(opt, 0.1);
             for (l2=1; l2<=(nlstate+ndeath);l2++){    
               if(l2==k2) continue;    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
               j=(k2-1)*(nlstate+ndeath)+l2;    d->function = func;
               if(j<=i) continue;    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
               for (age=bage; age<=fage; age ++){    nlopt_set_min_objective(opt, myfunc, d);
                 if ((int)age %5==0){    nlopt_set_xtol_rel(opt, ftol);
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;    if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;      printf("nlopt failed! %d\n",creturn); 
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;    }
                   mu1=mu[i][(int) age]/stepm*YEARM ;    else {
                   mu2=mu[j][(int) age]/stepm*YEARM;      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
                   /* Computing eigen value of matrix of covariance */      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));      iter=1; /* not equal */
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    }
                   if(first1==1){    nlopt_destroy(opt);
                     first1=0;  #endif
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);    free_matrix(xi,1,npar,1,npar);
                   }    fclose(ficrespow);
                   fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);    printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
                   /* Eigen vectors */    fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));    fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
                   v21=sqrt(1.-v11*v11);  
                   v12=-v21;  }
                   v22=v11;  
                   /*printf(fignu*/  /**** Computes Hessian and covariance matrix ***/
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */  {
                   if(first==1){    double  **a,**y,*x,pd;
                     first=0;    double **hess;
                     fprintf(ficgp,"\nset parametric;set nolabel");    int i, j;
                     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);    int *indx;
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");  
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);    void lubksb(double **a, int npar, int *indx, double b[]) ;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    void ludcmp(double **a, int npar, int *indx, double *d) ;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    double gompertz(double p[]);
                     /*              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\"",\    hess=matrix(1,npar,1,npar);
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \  
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    printf("\nCalculation of the hessian matrix. Wait...\n");
                     */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
                     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",\    for (i=1;i<=npar;i++){
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \      printf("%d",i);fflush(stdout);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));      fprintf(ficlog,"%d",i);fflush(ficlog);
                   }else{     
                     first=0;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);      
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);      /*  printf(" %f ",p[i]);
                     /*          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
                     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\"",\    }
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    for (i=1;i<=npar;i++) {
                     */      for (j=1;j<=npar;j++)  {
                     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",\        if (j>i) { 
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \          printf(".%d%d",i,j);fflush(stdout);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                   }/* if first */          hess[i][j]=hessij(p,delti,i,j,func,npar);
                 } /* age mod 5 */          
               } /* end loop age */          hess[j][i]=hess[i][j];    
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);          /*printf(" %lf ",hess[i][j]);*/
               first=1;        }
             } /*l12 */      }
           } /* k12 */    }
         } /*l1 */    printf("\n");
       }/* k1 */    fprintf(ficlog,"\n");
     } /* loop covariates */  
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);    a=matrix(1,npar,1,npar);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    y=matrix(1,npar,1,npar);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    x=vector(1,npar);
   }    indx=ivector(1,npar);
   free_vector(xp,1,npar);    for (i=1;i<=npar;i++)
   fclose(ficresprob);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   fclose(ficresprobcov);    ludcmp(a,npar,indx,&pd);
   fclose(ficresprobcor);  
   fclose(ficgp);    for (j=1;j<=npar;j++) {
   fclose(fichtm);      for (i=1;i<=npar;i++) x[i]=0;
 }      x[j]=1;
       lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
 /******************* Printing html file ***********/        matcov[i][j]=x[i];
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      }
                   int lastpass, int stepm, int weightopt, char model[],\    }
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\  
                   int popforecast, int estepm ,\    printf("\n#Hessian matrix#\n");
                   double jprev1, double mprev1,double anprev1, \    fprintf(ficlog,"\n#Hessian matrix#\n");
                   double jprev2, double mprev2,double anprev2){    for (i=1;i<=npar;i++) { 
   int jj1, k1, i1, cpt;      for (j=1;j<=npar;j++) { 
   /*char optionfilehtm[FILENAMELENGTH];*/        printf("%.3e ",hess[i][j]);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {        fprintf(ficlog,"%.3e ",hess[i][j]);
     printf("Problem with %s \n",optionfilehtm), exit(0);      }
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);      printf("\n");
   }      fprintf(ficlog,"\n");
     }
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n  
  - 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    /* Recompute Inverse */
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    for (i=1;i<=npar;i++)
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
  - Life expectancies by age and initial health status (estepm=%2d months):    ludcmp(a,npar,indx,&pd);
    <a href=\"e%s\">e%s</a> <br>\n</li>", \  
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    /*  printf("\n#Hessian matrix recomputed#\n");
   
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
  m=cptcoveff;      x[j]=1;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
  jj1=0;        y[i][j]=x[i];
  for(k1=1; k1<=m;k1++){        printf("%.3e ",y[i][j]);
    for(i1=1; i1<=ncodemax[k1];i1++){        fprintf(ficlog,"%.3e ",y[i][j]);
      jj1++;      }
      if (cptcovn > 0) {      printf("\n");
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      fprintf(ficlog,"\n");
        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\">");  
      }    free_matrix(a,1,npar,1,npar);
      /* Pij */    free_matrix(y,1,npar,1,npar);
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>    free_vector(x,1,npar);
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        free_ivector(indx,1,npar);
      /* Quasi-incidences */    free_matrix(hess,1,npar,1,npar);
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>  
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  
        /* Stable prevalence in each health state */  }
        for(cpt=1; cpt<nlstate;cpt++){  
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>  /*************** hessian matrix ****************/
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
        }  {
      for(cpt=1; cpt<=nlstate;cpt++) {    int i;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    int l=1, lmax=20;
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    double k1,k2;
      }    double p2[MAXPARM+1]; /* identical to x */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    double res;
 health expectancies in states (1) and (2): e%s%d.png<br>    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    double fx;
    } /* end i1 */    int k=0,kmax=10;
  }/* End k1 */    double l1;
  fprintf(fichtm,"</ul>");  
     fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n      l1=pow(10,l);
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      delts=delt;
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n      for(k=1 ; k <kmax; k=k+1){
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n        delt = delta*(l1*k);
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n        p2[theta]=x[theta] +delt;
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
  - 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);        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
  if(popforecast==1) fprintf(fichtm,"\n        /*res= (k1-2.0*fx+k2)/delt/delt; */
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n        
         <br>",fileres,fileres,fileres,fileres);  #ifdef DEBUGHESS
  else        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(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);        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(fichtm," <ul><li><b>Graphs</b></li><p>");  #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
  m=cptcoveff;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          k=kmax;
         }
  jj1=0;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
  for(k1=1; k1<=m;k1++){          k=kmax; l=lmax*10;
    for(i1=1; i1<=ncodemax[k1];i1++){        }
      jj1++;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
      if (cptcovn > 0) {          delts=delt;
        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\">");    delti[theta]=delts;
      }    return res; 
      for(cpt=1; cpt<=nlstate;cpt++) {    
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  }
 interval) in state (%d): v%s%d%d.png <br>  
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
      }  {
    } /* end i1 */    int i;
  }/* End k1 */    int l=1, lmax=20;
  fprintf(fichtm,"</ul>");    double k1,k2,k3,k4,res,fx;
 fclose(fichtm);    double p2[MAXPARM+1];
 }    int k;
   
 /******************* Gnuplot file **************/    fx=func(x);
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      p2[thetai]=x[thetai]+delti[thetai]/k;
   int ng;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {      k1=func(p2)-fx;
     printf("Problem with file %s",optionfilegnuplot);    
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);      p2[thetai]=x[thetai]+delti[thetai]/k;
   }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
 #ifdef windows    
     fprintf(ficgp,"cd \"%s\" \n",pathc);      p2[thetai]=x[thetai]-delti[thetai]/k;
 #endif      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 m=pow(2,cptcoveff);      k3=func(p2)-fx;
      
  /* 1eme*/      p2[thetai]=x[thetai]-delti[thetai]/k;
   for (cpt=1; cpt<= nlstate ; cpt ++) {      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
    for (k1=1; k1<= m ; k1 ++) {      k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 #ifdef windows  #ifdef DEBUG
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,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);
      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);      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  #endif
 #ifdef unix    }
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    return res;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);  }
 #endif  
   /************** Inverse of matrix **************/
 for (i=1; i<= nlstate ; i ++) {  void ludcmp(double **a, int n, int *indx, double *d) 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int i,imax,j,k; 
 }    double big,dum,sum,temp; 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    double *vv; 
     for (i=1; i<= nlstate ; i ++) {   
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    vv=vector(1,n); 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    *d=1.0; 
 }    for (i=1;i<=n;i++) { 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      big=0.0; 
      for (i=1; i<= nlstate ; i ++) {      for (j=1;j<=n;j++) 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        if ((temp=fabs(a[i][j])) > big) big=temp; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 }        vv[i]=1.0/big; 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    } 
 #ifdef unix    for (j=1;j<=n;j++) { 
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");      for (i=1;i<j;i++) { 
 #endif        sum=a[i][j]; 
    }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   }        a[i][j]=sum; 
   /*2 eme*/      } 
       big=0.0; 
   for (k1=1; k1<= m ; k1 ++) {      for (i=j;i<=n;i++) { 
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);        sum=a[i][j]; 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);        for (k=1;k<j;k++) 
              sum -= a[i][k]*a[k][j]; 
     for (i=1; i<= nlstate+1 ; i ++) {        a[i][j]=sum; 
       k=2*i;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          big=dum; 
       for (j=1; j<= nlstate+1 ; j ++) {          imax=i; 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      } 
 }        if (j != imax) { 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        for (k=1;k<=n;k++) { 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          dum=a[imax][k]; 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          a[imax][k]=a[j][k]; 
       for (j=1; j<= nlstate+1 ; j ++) {          a[j][k]=dum; 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        } 
         else fprintf(ficgp," \%%*lf (\%%*lf)");        *d = -(*d); 
 }          vv[imax]=vv[j]; 
       fprintf(ficgp,"\" t\"\" w l 0,");      } 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      indx[j]=imax; 
       for (j=1; j<= nlstate+1 ; j ++) {      if (a[j][j] == 0.0) a[j][j]=TINY; 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      if (j != n) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");        dum=1.0/(a[j][j]); 
 }          for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      } 
       else fprintf(ficgp,"\" t\"\" w l 0,");    } 
     }    free_vector(vv,1,n);  /* Doesn't work */
   }  ;
    } 
   /*3eme*/  
   void lubksb(double **a, int n, int *indx, double b[]) 
   for (k1=1; k1<= m ; k1 ++) {  { 
     for (cpt=1; cpt<= nlstate ; cpt ++) {    int i,ii=0,ip,j; 
       k=2+nlstate*(2*cpt-2);    double sum; 
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);   
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    for (i=1;i<=n;i++) { 
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      ip=indx[i]; 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      sum=b[ip]; 
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      b[ip]=b[i]; 
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      if (ii) 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      else if (sum) ii=i; 
       b[i]=sum; 
 */    } 
       for (i=1; i< nlstate ; i ++) {    for (i=n;i>=1;i--) { 
         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);      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       }      b[i]=sum/a[i][i]; 
     }    } 
   }  } 
    
   /* CV preval stat */  void pstamp(FILE *fichier)
     for (k1=1; k1<= m ; k1 ++) {  {
     for (cpt=1; cpt<nlstate ; cpt ++) {    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
       k=3;  }
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);  /************ Frequencies ********************/
   void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
       for (i=1; i< nlstate ; i ++)  {  /* Some frequencies */
         fprintf(ficgp,"+$%d",k+i+1);    
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    int i, m, jk, j1, bool, z1,j;
          int first;
       l=3+(nlstate+ndeath)*cpt;    double ***freq; /* Frequencies */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    double *pp, **prop;
       for (i=1; i< nlstate ; i ++) {    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         l=3+(nlstate+ndeath)*cpt;    char fileresp[FILENAMELENGTH];
         fprintf(ficgp,"+$%d",l+i+1);    
       }    pp=vector(1,nlstate);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      prop=matrix(1,nlstate,iagemin,iagemax+3);
     }    strcpy(fileresp,"p");
   }      strcat(fileresp,fileres);
      if((ficresp=fopen(fileresp,"w"))==NULL) {
   /* proba elementaires */      printf("Problem with prevalence resultfile: %s\n", fileresp);
    for(i=1,jk=1; i <=nlstate; i++){      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     for(k=1; k <=(nlstate+ndeath); k++){      exit(0);
       if (k != i) {    }
         for(j=1; j <=ncovmodel; j++){    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    j1=0;
           jk++;    
           fprintf(ficgp,"\n");    j=cptcoveff;
         }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       }  
     }    first=1;
    }  
     /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
      for(jk=1; jk <=m; jk++) {    /*    j1++; */
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
        if (ng==2)        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");          scanf("%d", i);*/
        else        for (i=-5; i<=nlstate+ndeath; i++)  
          fprintf(ficgp,"\nset title \"Probability\"\n");          for (jk=-5; jk<=nlstate+ndeath; jk++)  
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);            for(m=iagemin; m <= iagemax+3; m++)
        i=1;              freq[i][jk][m]=0;
        for(k2=1; k2<=nlstate; k2++) {        
          k3=i;        for (i=1; i<=nlstate; i++)  
          for(k=1; k<=(nlstate+ndeath); k++) {          for(m=iagemin; m <= iagemax+3; m++)
            if (k != k2){            prop[i][m]=0;
              if(ng==2)        
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);        dateintsum=0;
              else        k2cpt=0;
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        for (i=1; i<=imx; i++) {
              ij=1;          bool=1;
              for(j=3; j <=ncovmodel; j++) {          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            for (z1=1; z1<=cptcoveff; z1++)       
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
                  ij++;                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
                }                bool=0;
                else                /* 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,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
              }                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
              fprintf(ficgp,")/(1");                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
                            } 
              for(k1=1; k1 <=nlstate; k1++){            }
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);   
                ij=1;          if (bool==1){
                for(j=3; j <=ncovmodel; j++){            for(m=firstpass; m<=lastpass; m++){
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              k2=anint[m][i]+(mint[m][i]/12.);
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                    ij++;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                  }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                  else                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                if (m<lastpass) {
                }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                fprintf(ficgp,")");                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
              }                }
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);                
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
              i=i+ncovmodel;                  dateintsum=dateintsum+k2;
            }                  k2cpt++;
          } /* end k */                }
        } /* end k2 */                /*}*/
      } /* end jk */            }
    } /* end ng */          }
    fclose(ficgp);        } /* end i */
 }  /* end gnuplot */         
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         pstamp(ficresp);
 /*************** Moving average **************/        if  (cptcovn>0) {
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   int i, cpt, cptcod;          fprintf(ficresp, "**********\n#");
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          fprintf(ficlog, "\n#********** Variable "); 
       for (i=1; i<=nlstate;i++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          fprintf(ficlog, "**********\n#");
           mobaverage[(int)agedeb][i][cptcod]=0.;        }
            for(i=1; i<=nlstate;i++) 
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       for (i=1; i<=nlstate;i++){        fprintf(ficresp, "\n");
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        
           for (cpt=0;cpt<=4;cpt++){        for(i=iagemin; i <= iagemax+3; i++){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          if(i==iagemax+3){
           }            fprintf(ficlog,"Total");
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          }else{
         }            if(first==1){
       }              first=0;
     }              printf("See log file for details...\n");
                }
 }            fprintf(ficlog,"Age %d", i);
           }
           for(jk=1; jk <=nlstate ; jk++){
 /************** Forecasting ******************/            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 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){              pp[jk] += freq[jk][m][i]; 
            }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          for(jk=1; jk <=nlstate ; jk++){
   int *popage;            for(m=-1, pos=0; m <=0 ; m++)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              pos += freq[jk][m][i];
   double *popeffectif,*popcount;            if(pp[jk]>=1.e-10){
   double ***p3mat;              if(first==1){
   char fileresf[FILENAMELENGTH];                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
  agelim=AGESUP;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;            }else{
               if(first==1)
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
              }
   strcpy(fileresf,"f");          }
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {          for(jk=1; jk <=nlstate ; jk++){
     printf("Problem with forecast resultfile: %s\n", fileresf);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);              pp[jk] += freq[jk][m][i];
   }          }       
   printf("Computing forecasting: result on file '%s' \n", fileresf);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);            pos += pp[jk];
             posprop += prop[jk][i];
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          }
           for(jk=1; jk <=nlstate ; jk++){
   if (mobilav==1) {            if(pos>=1.e-5){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              if(first==1)
     movingaverage(agedeb, fage, ageminpar, mobaverage);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
   stepsize=(int) (stepm+YEARM-1)/YEARM;              if(first==1)
   if (stepm<=12) stepsize=1;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   agelim=AGESUP;            }
              if( i <= iagemax){
   hstepm=1;              if(pos>=1.e-5){
   hstepm=hstepm/stepm;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   yp1=modf(dateintmean,&yp);                /*probs[i][jk][j1]= pp[jk]/pos;*/
   anprojmean=yp;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   yp2=modf((yp1*12),&yp);              }
   mprojmean=yp;              else
   yp1=modf((yp2*30.5),&yp);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   jprojmean=yp;            }
   if(jprojmean==0) jprojmean=1;          }
   if(mprojmean==0) jprojmean=1;          
            for(jk=-1; jk <=nlstate+ndeath; jk++)
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);            for(m=-1; m <=nlstate+ndeath; m++)
                if(freq[jk][m][i] !=0 ) {
   for(cptcov=1;cptcov<=i2;cptcov++){              if(first==1)
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       k=k+1;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       fprintf(ficresf,"\n#******");              }
       for(j=1;j<=cptcoveff;j++) {          if(i <= iagemax)
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficresp,"\n");
       }          if(first==1)
       fprintf(ficresf,"******\n");            printf("Others in log...\n");
       fprintf(ficresf,"# StartingAge FinalAge");          fprintf(ficlog,"\n");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        }
              /*}*/
          }
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    dateintmean=dateintsum/k2cpt; 
         fprintf(ficresf,"\n");   
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      fclose(ficresp);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    free_vector(pp,1,nlstate);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
           nhstepm = nhstepm/hstepm;    /* End of Freq */
            }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;  /************ Prevalence ********************/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
          {  
           for (h=0; h<=nhstepm; h++){    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
             if (h==(int) (calagedate+YEARM*cpt)) {       in each health status at the date of interview (if between dateprev1 and dateprev2).
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);       We still use firstpass and lastpass as another selection.
             }    */
             for(j=1; j<=nlstate+ndeath;j++) {   
               kk1=0.;kk2=0;    int i, m, jk, j1, bool, z1,j;
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)    double **prop;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    double posprop; 
                 else {    double  y2; /* in fractional years */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    int iagemin, iagemax;
                 }    int first; /** to stop verbosity which is redirected to log file */
                  
               }    iagemin= (int) agemin;
               if (h==(int)(calagedate+12*cpt)){    iagemax= (int) agemax;
                 fprintf(ficresf," %.3f", kk1);    /*pp=vector(1,nlstate);*/
                            prop=matrix(1,nlstate,iagemin,iagemax+3); 
               }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
             }    j1=0;
           }    
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*j=cptcoveff;*/
         }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       }    
     }    first=1;
   }    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
              /*for(i1=1; i1<=ncodemax[k1];i1++){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        j1++;*/
         
   fclose(ficresf);        for (i=1; i<=nlstate; i++)  
 }          for(m=iagemin; m <= iagemax+3; m++)
 /************** Forecasting ******************/            prop[i][m]=0.0;
 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){       
          for (i=1; i<=imx; i++) { /* Each individual */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          bool=1;
   int *popage;          if  (cptcovn>0) {
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            for (z1=1; z1<=cptcoveff; z1++) 
   double *popeffectif,*popcount;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   double ***p3mat,***tabpop,***tabpopprev;                bool=0;
   char filerespop[FILENAMELENGTH];          } 
           if (bool==1) { 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   agelim=AGESUP;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                  if (s[m][i]>0 && s[m][i]<=nlstate) { 
                    /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
   strcpy(filerespop,"pop");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   strcat(filerespop,fileres);                  prop[s[m][i]][iagemax+3] += weight[i]; 
   if((ficrespop=fopen(filerespop,"w"))==NULL) {                } 
     printf("Problem with forecast resultfile: %s\n", filerespop);              }
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);            } /* end selection of waves */
   }          }
   printf("Computing forecasting: result on file '%s' \n", filerespop);        }
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);        for(i=iagemin; i <= iagemax+3; i++){  
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            posprop += prop[jk][i]; 
           } 
   if (mobilav==1) {          
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(jk=1; jk <=nlstate ; jk++){     
     movingaverage(agedeb, fage, ageminpar, mobaverage);            if( i <=  iagemax){ 
   }              if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
   stepsize=(int) (stepm+YEARM-1)/YEARM;              } else{
   if (stepm<=12) stepsize=1;                if(first==1){
                    first=0;
   agelim=AGESUP;                  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]);
                  }
   hstepm=1;              }
   hstepm=hstepm/stepm;            } 
            }/* end jk */ 
   if (popforecast==1) {        }/* end i */ 
     if((ficpop=fopen(popfile,"r"))==NULL) {      /*} *//* end i1 */
       printf("Problem with population file : %s\n",popfile);exit(0);    } /* end j1 */
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);    
     }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     popage=ivector(0,AGESUP);    /*free_vector(pp,1,nlstate);*/
     popeffectif=vector(0,AGESUP);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     popcount=vector(0,AGESUP);  }  /* End of prevalence */
      
     i=1;    /************* Waves Concatenation ***************/
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  
      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)
     imx=i;  {
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   }       Death is a valid wave (if date is known).
        mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   for(cptcov=1;cptcov<=i2;cptcov++){       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       and mw[mi+1][i]. dh depends on stepm.
       k=k+1;       */
       fprintf(ficrespop,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {    int i, mi, m;
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       }       double sum=0., jmean=0.;*/
       fprintf(ficrespop,"******\n");    int first;
       fprintf(ficrespop,"# Age");    int j, k=0,jk, ju, jl;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    double sum=0.;
       if (popforecast==1)  fprintf(ficrespop," [Population]");    first=0;
          jmin=100000;
       for (cpt=0; cpt<=0;cpt++) {    jmax=-1;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      jmean=0.;
            for(i=1; i<=imx; i++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      mi=0;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      m=firstpass;
           nhstepm = nhstepm/hstepm;      while(s[m][i] <= nlstate){
                  if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          mw[++mi][i]=m;
           oldm=oldms;savm=savms;        if(m >=lastpass)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            break;
                else
           for (h=0; h<=nhstepm; h++){          m++;
             if (h==(int) (calagedate+YEARM*cpt)) {      }/* end while */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      if (s[m][i] > nlstate){
             }        mi++;     /* Death is another wave */
             for(j=1; j<=nlstate+ndeath;j++) {        /* if(mi==0)  never been interviewed correctly before death */
               kk1=0.;kk2=0;           /* Only death is a correct wave */
               for(i=1; i<=nlstate;i++) {                      mw[mi][i]=m;
                 if (mobilav==1)      }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {      wav[i]=mi;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      if(mi==0){
                 }        nbwarn++;
               }        if(first==0){
               if (h==(int)(calagedate+12*cpt)){          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          first=1;
                   /*fprintf(ficrespop," %.3f", kk1);        }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        if(first==1){
               }          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
             }        }
             for(i=1; i<=nlstate;i++){      } /* end mi==0 */
               kk1=0.;    } /* End individuals */
                 for(j=1; j<=nlstate;j++){  
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    for(i=1; i<=imx; i++){
                 }      for(mi=1; mi<wav[i];mi++){
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        if (stepm <=0)
             }          dh[mi][i]=1;
         else{
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);            if (agedc[i] < 2*AGESUP) {
           }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              if(j==0) j=1;  /* Survives at least one month after exam */
         }              else if(j<0){
       }                nberr++;
                  printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   /******/                j=1; /* Temporary Dangerous patch */
                 printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                  fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              k=k+1;
           nhstepm = nhstepm/hstepm;              if (j >= jmax){
                          jmax=j;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                ijmax=i;
           oldm=oldms;savm=savms;              }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                if (j <= jmin){
           for (h=0; h<=nhstepm; h++){                jmin=j;
             if (h==(int) (calagedate+YEARM*cpt)) {                ijmin=i;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);              }
             }              sum=sum+j;
             for(j=1; j<=nlstate+ndeath;j++) {              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               kk1=0.;kk2=0;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
               for(i=1; i<=nlstate;i++) {                          }
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              }
               }          else{
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);            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]); */
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            k=k+1;
         }            if (j >= jmax) {
       }              jmax=j;
    }              ijmax=i;
   }            }
              else if (j <= jmin){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              jmin=j;
               ijmin=i;
   if (popforecast==1) {            }
     free_ivector(popage,0,AGESUP);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     free_vector(popeffectif,0,AGESUP);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
     free_vector(popcount,0,AGESUP);            if(j<0){
   }              nberr++;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              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]);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              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]);
   fclose(ficrespop);            }
 }            sum=sum+j;
           }
 /***********************************************/          jk= j/stepm;
 /**************** Main Program *****************/          jl= j -jk*stepm;
 /***********************************************/          ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
 int main(int argc, char *argv[])            if(jl==0){
 {              dh[mi][i]=jk;
               bh[mi][i]=0;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;            }else{ /* We want a negative bias in order to only have interpolation ie
   double agedeb, agefin,hf;                    * to avoid the price of an extra matrix product in likelihood */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
   double fret;            }
   double **xi,tmp,delta;          }else{
             if(jl <= -ju){
   double dum; /* Dummy variable */              dh[mi][i]=jk;
   double ***p3mat;              bh[mi][i]=jl;       /* bias is positive if real duration
   int *indx;                                   * is higher than the multiple of stepm and negative otherwise.
   char line[MAXLINE], linepar[MAXLINE];                                   */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];            }
   int firstobs=1, lastobs=10;            else{
   int sdeb, sfin; /* Status at beginning and end */              dh[mi][i]=jk+1;
   int c,  h , cpt,l;              bh[mi][i]=ju;
   int ju,jl, mi;            }
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            if(dh[mi][i]==0){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;              dh[mi][i]=1; /* At least one step */
   int mobilav=0,popforecast=0;              bh[mi][i]=ju; /* At least one step */
   int hstepm, nhstepm;              /*  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);*/
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;            }
           } /* end if mle */
   double bage, fage, age, agelim, agebase;        }
   double ftolpl=FTOL;      } /* end wave */
   double **prlim;    }
   double *severity;    jmean=sum/k;
   double ***param; /* Matrix of parameters */    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);
   double  *p;    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);
   double **matcov; /* Matrix of covariance */   }
   double ***delti3; /* Scale */  
   double *delti; /* Scale */  /*********** Tricode ****************************/
   double ***eij, ***vareij;  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   double **varpl; /* Variances of prevalence limits by age */  {
   double *epj, vepp;    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   double kk1, kk2;    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;     * Boring subroutine which should only output nbcode[Tvar[j]][k]
       * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
      * nbcode[Tvar[j]][1]= 
   char *alph[]={"a","a","b","c","d","e"}, str[4];    */
   
     int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   char z[1]="c", occ;    int modmaxcovj=0; /* Modality max of covariates j */
 #include <sys/time.h>    int cptcode=0; /* Modality max of covariates j */
 #include <time.h>    int modmincovj=0; /* Modality min of covariates j */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
    
   /* long total_usecs;    cptcoveff=0; 
   struct timeval start_time, end_time;   
      for (k=-1; k < maxncov; k++) Ndum[k]=0;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   getcwd(pathcd, size);  
     /* Loop on covariates without age and products */
   printf("\n%s",version);    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
   if(argc <=1){      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
     printf("\nEnter the parameter file name: ");                                 modality of this covariate Vj*/ 
     scanf("%s",pathtot);        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 *:
   else{                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
     strcpy(pathtot,argv[1]);                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
   }        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/                                        modality of the nth covariate of individual i. */
   /*cygwin_split_path(pathtot,path,optionfile);        if (ij > modmaxcovj)
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          modmaxcovj=ij; 
   /* cutv(path,optionfile,pathtot,'\\');*/        else if (ij < modmincovj) 
           modmincovj=ij; 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        if ((ij < -1) && (ij > NCOVMAX)){
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   chdir(path);          exit(1);
   replace(pathc,path);        }else
         Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
 /*-------- arguments in the command line --------*/        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   /* Log file */        /* getting the maximum value of the modality of the covariate
   strcat(filelog, optionfilefiname);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
   strcat(filelog,".log");    /* */           female is 1, then modmaxcovj=1.*/
   if((ficlog=fopen(filelog,"w"))==NULL)    {      }
     printf("Problem with logfile %s\n",filelog);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
     goto end;      cptcode=modmaxcovj;
   }      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
   fprintf(ficlog,"Log filename:%s\n",filelog);     /*for (i=0; i<=cptcode; i++) {*/
   fprintf(ficlog,"\n%s",version);      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
   fprintf(ficlog,"\nEnter the parameter file name: ");        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
   fflush(ficlog);          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
         }
   /* */        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
   strcpy(fileres,"r");           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
   strcat(fileres, optionfilefiname);      } /* Ndum[-1] number of undefined modalities */
   strcat(fileres,".txt");    /* Other files have txt extension */  
       /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
   /*---------arguments file --------*/      /* 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;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {         modmincovj=3; modmaxcovj = 7;
     printf("Problem with optionfile %s\n",optionfile);         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
     goto end;         variables V1_1 and V1_2.
   }         nbcode[Tvar[j]][ij]=k;
          nbcode[Tvar[j]][1]=0;
   strcpy(filereso,"o");         nbcode[Tvar[j]][2]=1;
   strcat(filereso,fileres);         nbcode[Tvar[j]][3]=2;
   if((ficparo=fopen(filereso,"w"))==NULL) {      */
     printf("Problem with Output resultfile: %s\n", filereso);      ij=1; /* ij is similar to i but can jumps over null modalities */
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
     goto end;        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
   }          /*recode from 0 */
           if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
   /* Reads comments: lines beginning with '#' */            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
   while((c=getc(ficpar))=='#' && c!= EOF){                                       k is a modality. If we have model=V1+V1*sex 
     ungetc(c,ficpar);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     fgets(line, MAXLINE, ficpar);            ij++;
     puts(line);          }
     fputs(line,ficparo);          if (ij > ncodemax[j]) break; 
   }        }  /* end of loop on */
   ungetc(c,ficpar);      } /* end of loop on modality */ 
     } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   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);    
   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);   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);    
 while((c=getc(ficpar))=='#' && c!= EOF){    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
     ungetc(c,ficpar);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
     fgets(line, MAXLINE, ficpar);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
     puts(line);     Ndum[ij]++; 
     fputs(line,ficparo);   } 
   }  
   ungetc(c,ficpar);   ij=1;
     for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
         /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   covar=matrix(0,NCOVMAX,1,n);     if((Ndum[i]!=0) && (i<=ncovcol)){
   cptcovn=0;       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;       Tvaraff[ij]=i; /*For printing (unclear) */
        ij++;
   ncovmodel=2+cptcovn;     }else
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */         Tvaraff[ij]=0;
     }
   /* Read guess parameters */   ij--;
   /* Reads comments: lines beginning with '#' */   cptcoveff=ij; /*Number of total covariates*/
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  }
     fgets(line, MAXLINE, ficpar);  
     puts(line);  
     fputs(line,ficparo);  /*********** Health Expectancies ****************/
   }  
   ungetc(c,ficpar);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  {
     for(i=1; i <=nlstate; i++)    /* Health expectancies, no variances */
     for(j=1; j <=nlstate+ndeath-1; j++){    int i, j, nhstepm, hstepm, h, nstepm;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    int nhstepma, nstepma; /* Decreasing with age */
       fprintf(ficparo,"%1d%1d",i1,j1);    double age, agelim, hf;
       if(mle==1)    double ***p3mat;
         printf("%1d%1d",i,j);    double eip;
       fprintf(ficlog,"%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){    pstamp(ficreseij);
         fscanf(ficpar," %lf",&param[i][j][k]);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
         if(mle==1){    fprintf(ficreseij,"# Age");
           printf(" %lf",param[i][j][k]);    for(i=1; i<=nlstate;i++){
           fprintf(ficlog," %lf",param[i][j][k]);      for(j=1; j<=nlstate;j++){
         }        fprintf(ficreseij," e%1d%1d ",i,j);
         else      }
           fprintf(ficlog," %lf",param[i][j][k]);      fprintf(ficreseij," e%1d. ",i);
         fprintf(ficparo," %lf",param[i][j][k]);    }
       }    fprintf(ficreseij,"\n");
       fscanf(ficpar,"\n");  
       if(mle==1)    
         printf("\n");    if(estepm < stepm){
       fprintf(ficlog,"\n");      printf ("Problem %d lower than %d\n",estepm, stepm);
       fprintf(ficparo,"\n");    }
     }    else  hstepm=estepm;   
      /* We compute the life expectancy from trapezoids spaced every estepm months
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;     * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
   p=param[1][1];     * we are calculating an estimate of the Life Expectancy assuming a linear 
       * progression in between and thus overestimating or underestimating according
   /* Reads comments: lines beginning with '#' */     * to the curvature of the survival function. If, for the same date, we 
   while((c=getc(ficpar))=='#' && c!= EOF){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     ungetc(c,ficpar);     * to compare the new estimate of Life expectancy with the same linear 
     fgets(line, MAXLINE, ficpar);     * hypothesis. A more precise result, taking into account a more precise
     puts(line);     * curvature will be obtained if estepm is as small as stepm. */
     fputs(line,ficparo);  
   }    /* For example we decided to compute the life expectancy with the smallest unit */
   ungetc(c,ficpar);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       nstepm is the number of stepm from age to agelin. 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */       Look at hpijx to understand the reason of that which relies in memory size
   for(i=1; i <=nlstate; i++){       and note for a fixed period like estepm months */
     for(j=1; j <=nlstate+ndeath-1; j++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       fscanf(ficpar,"%1d%1d",&i1,&j1);       survival function given by stepm (the optimization length). Unfortunately it
       printf("%1d%1d",i,j);       means that if the survival funtion is printed only each two years of age and if
       fprintf(ficparo,"%1d%1d",i1,j1);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       for(k=1; k<=ncovmodel;k++){       results. So we changed our mind and took the option of the best precision.
         fscanf(ficpar,"%le",&delti3[i][j][k]);    */
         printf(" %le",delti3[i][j][k]);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }    agelim=AGESUP;
       fscanf(ficpar,"\n");    /* If stepm=6 months */
       printf("\n");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       fprintf(ficparo,"\n");         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     }      
   }  /* nhstepm age range expressed in number of stepm */
   delti=delti3[1][1];    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   /* Reads comments: lines beginning with '#' */    /* if (stepm >= YEARM) hstepm=1;*/
   while((c=getc(ficpar))=='#' && c!= EOF){    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     ungetc(c,ficpar);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fgets(line, MAXLINE, ficpar);  
     puts(line);    for (age=bage; age<=fage; age ++){ 
     fputs(line,ficparo);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   ungetc(c,ficpar);      /* if (stepm >= YEARM) hstepm=1;*/
        nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   matcov=matrix(1,npar,1,npar);  
   for(i=1; i <=npar; i++){      /* If stepm=6 months */
     fscanf(ficpar,"%s",&str);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     if(mle==1)         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       printf("%s",str);      
     fprintf(ficlog,"%s",str);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     fprintf(ficparo,"%s",str);      
     for(j=1; j <=i; j++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       fscanf(ficpar," %le",&matcov[i][j]);      
       if(mle==1){      printf("%d|",(int)age);fflush(stdout);
         printf(" %.5le",matcov[i][j]);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         fprintf(ficlog," %.5le",matcov[i][j]);      
       }      /* Computing expectancies */
       else      for(i=1; i<=nlstate;i++)
         fprintf(ficlog," %.5le",matcov[i][j]);        for(j=1; j<=nlstate;j++)
       fprintf(ficparo," %.5le",matcov[i][j]);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     }            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     fscanf(ficpar,"\n");            
     if(mle==1)            /* 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]);*/
       printf("\n");  
     fprintf(ficlog,"\n");          }
     fprintf(ficparo,"\n");  
   }      fprintf(ficreseij,"%3.0f",age );
   for(i=1; i <=npar; i++)      for(i=1; i<=nlstate;i++){
     for(j=i+1;j<=npar;j++)        eip=0;
       matcov[i][j]=matcov[j][i];        for(j=1; j<=nlstate;j++){
              eip +=eij[i][j][(int)age];
   if(mle==1)          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
     printf("\n");        }
   fprintf(ficlog,"\n");        fprintf(ficreseij,"%9.4f", eip );
       }
       fprintf(ficreseij,"\n");
     /*-------- Rewriting paramater file ----------*/      
      strcpy(rfileres,"r");    /* "Rparameterfile */    }
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      strcat(rfileres,".");    /* */    printf("\n");
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    fprintf(ficlog,"\n");
     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;  
     }  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
     fprintf(ficres,"#%s\n",version);  
      {
     /*-------- data file ----------*/    /* Covariances of health expectancies eij and of total life expectancies according
     if((fic=fopen(datafile,"r"))==NULL)    {     to initial status i, ei. .
       printf("Problem with datafile: %s\n", datafile);goto end;    */
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     }    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
     n= lastobs;    double ***p3matp, ***p3matm, ***varhe;
     severity = vector(1,maxwav);    double **dnewm,**doldm;
     outcome=imatrix(1,maxwav+1,1,n);    double *xp, *xm;
     num=ivector(1,n);    double **gp, **gm;
     moisnais=vector(1,n);    double ***gradg, ***trgradg;
     annais=vector(1,n);    int theta;
     moisdc=vector(1,n);  
     andc=vector(1,n);    double eip, vip;
     agedc=vector(1,n);  
     cod=ivector(1,n);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     weight=vector(1,n);    xp=vector(1,npar);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    xm=vector(1,npar);
     mint=matrix(1,maxwav,1,n);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     anint=matrix(1,maxwav,1,n);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     s=imatrix(1,maxwav+1,1,n);    
     adl=imatrix(1,maxwav+1,1,n);        pstamp(ficresstdeij);
     tab=ivector(1,NCOVMAX);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     ncodemax=ivector(1,8);    fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
     i=1;      for(j=1; j<=nlstate;j++)
     while (fgets(line, MAXLINE, fic) != NULL)    {        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       if ((i >= firstobs) && (i <=lastobs)) {      fprintf(ficresstdeij," e%1d. ",i);
            }
         for (j=maxwav;j>=1;j--){    fprintf(ficresstdeij,"\n");
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  
           strcpy(line,stra);    pstamp(ficrescveij);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficrescveij,"# Age");
         }    for(i=1; i<=nlstate;i++)
              for(j=1; j<=nlstate;j++){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        cptj= (j-1)*nlstate+i;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        for(i2=1; i2<=nlstate;i2++)
           for(j2=1; j2<=nlstate;j2++){
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            cptj2= (j2-1)*nlstate+i2;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            if(cptj2 <= cptj)
               fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          }
         for (j=ncovcol;j>=1;j--){      }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficrescveij,"\n");
         }    
         num[i]=atol(stra);    if(estepm < stepm){
              printf ("Problem %d lower than %d\n",estepm, stepm);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    }
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
         i=i+1;     * This is mainly to measure the difference between two models: for example
       }     * if stepm=24 months pijx are given only every 2 years and by summing them
     }     * we are calculating an estimate of the Life Expectancy assuming a linear 
     /* printf("ii=%d", ij);     * progression in between and thus overestimating or underestimating according
        scanf("%d",i);*/     * to the curvature of the survival function. If, for the same date, we 
   imx=i-1; /* Number of individuals */     * 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 
   /* for (i=1; i<=imx; i++){     * hypothesis. A more precise result, taking into account a more precise
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;     * curvature will be obtained if estepm is as small as stepm. */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;  
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    /* For example we decided to compute the life expectancy with the smallest unit */
     }*/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
    /*  for (i=1; i<=imx; i++){       nhstepm is the number of hstepm from age to agelim 
      if (s[4][i]==9)  s[4][i]=-1;       nstepm is the number of stepm from age to agelin. 
      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]));}*/       Look at hpijx to understand the reason of that which relies in memory size
         and note for a fixed period like estepm months */
      /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   /* Calculation of the number of parameter from char model*/       survival function given by stepm (the optimization length). Unfortunately it
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */       means that if the survival funtion is printed only each two years of age and if
   Tprod=ivector(1,15);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   Tvaraff=ivector(1,15);       results. So we changed our mind and took the option of the best precision.
   Tvard=imatrix(1,15,1,2);    */
   Tage=ivector(1,15);          hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      
   if (strlen(model) >1){    /* If stepm=6 months */
     j=0, j1=0, k1=1, k2=1;    /* nhstepm age range expressed in number of stepm */
     j=nbocc(model,'+');    agelim=AGESUP;
     j1=nbocc(model,'*');    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     cptcovn=j+1;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     cptcovprod=j1;    /* if (stepm >= YEARM) hstepm=1;*/
        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     strcpy(modelsav,model);    
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       printf("Error. Non available option model=%s ",model);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficlog,"Error. Non available option model=%s ",model);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       goto end;    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     }    gp=matrix(0,nhstepm,1,nlstate*nlstate);
        gm=matrix(0,nhstepm,1,nlstate*nlstate);
     for(i=(j+1); i>=1;i--){  
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */    for (age=bage; age<=fage; age ++){ 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /*scanf("%d",i);*/      /* if (stepm >= YEARM) hstepm=1;*/
       if (strchr(strb,'*')) {  /* Model includes a product */      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/  
         if (strcmp(strc,"age")==0) { /* Vn*age */      /* If stepm=6 months */
           cptcovprod--;      /* Computed by stepm unit matrices, product of hstepma matrices, stored
           cutv(strb,stre,strd,'V');         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/      
           cptcovage++;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/      /* Computing  Variances of health expectancies */
         }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
         else if (strcmp(strd,"age")==0) { /* or age*Vn */         decrease memory allocation */
           cptcovprod--;      for(theta=1; theta <=npar; theta++){
           cutv(strb,stre,strc,'V');        for(i=1; i<=npar; i++){ 
           Tvar[i]=atoi(stre);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           cptcovage++;          xm[i] = x[i] - (i==theta ?delti[theta]:0);
           Tage[cptcovage]=i;        }
         }        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         else {  /* Age is not in the model */        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/    
           Tvar[i]=ncovcol+k1;        for(j=1; j<= nlstate; j++){
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */          for(i=1; i<=nlstate; i++){
           Tprod[k1]=i;            for(h=0; h<=nhstepm-1; h++){
           Tvard[k1][1]=atoi(strc); /* m*/              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
           Tvard[k1][2]=atoi(stre); /* n */              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
           Tvar[cptcovn+k2]=Tvard[k1][1];            }
           Tvar[cptcovn+k2+1]=Tvard[k1][2];          }
           for (k=1; k<=lastobs;k++)        }
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];       
           k1++;        for(ij=1; ij<= nlstate*nlstate; ij++)
           k2=k2+2;          for(h=0; h<=nhstepm-1; h++){
         }            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
       }          }
       else { /* no more sum */      }/* End theta */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      
        /*  scanf("%d",i);*/      
       cutv(strd,strc,strb,'V');      for(h=0; h<=nhstepm-1; h++)
       Tvar[i]=atoi(strc);        for(j=1; j<=nlstate*nlstate;j++)
       }          for(theta=1; theta <=npar; theta++)
       strcpy(modelsav,stra);              trgradg[h][j][theta]=gradg[h][theta][j];
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      
         scanf("%d",i);*/  
     } /* end of loop + */       for(ij=1;ij<=nlstate*nlstate;ij++)
   } /* end model */        for(ji=1;ji<=nlstate*nlstate;ji++)
            varhe[ij][ji][(int)age] =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);       printf("%d|",(int)age);fflush(stdout);
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   scanf("%d ",i);*/       for(h=0;h<=nhstepm-1;h++){
     fclose(fic);        for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     /*  if(mle==1){*/          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     if (weightopt != 1) { /* Maximisation without weights*/          for(ij=1;ij<=nlstate*nlstate;ij++)
       for(i=1;i<=n;i++) weight[i]=1.0;            for(ji=1;ji<=nlstate*nlstate;ji++)
     }              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     /*-calculation of age at interview from date of interview and age at death -*/        }
     agev=matrix(1,maxwav,1,imx);      }
   
     for (i=1; i<=imx; i++) {      /* Computing expectancies */
       for(m=2; (m<= maxwav); m++) {      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      for(i=1; i<=nlstate;i++)
          anint[m][i]=9999;        for(j=1; j<=nlstate;j++)
          s[m][i]=-1;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
        }            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;            
       }            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     }  
           }
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      fprintf(ficresstdeij,"%3.0f",age );
       for(m=1; (m<= maxwav); m++){      for(i=1; i<=nlstate;i++){
         if(s[m][i] >0){        eip=0.;
           if (s[m][i] >= nlstate+1) {        vip=0.;
             if(agedc[i]>0)        for(j=1; j<=nlstate;j++){
               if(moisdc[i]!=99 && andc[i]!=9999)          eip += eij[i][j][(int)age];
                 agev[m][i]=agedc[i];          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
            else {          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
               if (andc[i]!=9999){        }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);      }
               agev[m][i]=-1;      fprintf(ficresstdeij,"\n");
               }  
             }      fprintf(ficrescveij,"%3.0f",age );
           }      for(i=1; i<=nlstate;i++)
           else if(s[m][i] !=9){ /* Should no more exist */        for(j=1; j<=nlstate;j++){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          cptj= (j-1)*nlstate+i;
             if(mint[m][i]==99 || anint[m][i]==9999)          for(i2=1; i2<=nlstate;i2++)
               agev[m][i]=1;            for(j2=1; j2<=nlstate;j2++){
             else if(agev[m][i] <agemin){              cptj2= (j2-1)*nlstate+i2;
               agemin=agev[m][i];              if(cptj2 <= cptj)
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }            }
             else if(agev[m][i] >agemax){        }
               agemax=agev[m][i];      fprintf(ficrescveij,"\n");
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/     
             }    }
             /*agev[m][i]=anint[m][i]-annais[i];*/    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
             /*   agev[m][i] = age[i]+2*m;*/    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
           }    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
           else { /* =9 */    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
             agev[m][i]=1;    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             s[m][i]=-1;    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }    printf("\n");
         }    fprintf(ficlog,"\n");
         else /*= 0 Unknown */  
           agev[m][i]=1;    free_vector(xm,1,npar);
       }    free_vector(xp,1,npar);
        free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     for (i=1; i<=imx; i++)  {    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       for(m=1; (m<= maxwav); m++){  }
         if (s[m][i] > (nlstate+ndeath)) {  
           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);    /************ Variance ******************/
           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);    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[])
           goto end;  {
         }    /* Variance of health expectancies */
       }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     }    /* double **newm;*/
     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
 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);    int movingaverage();
     double **dnewm,**doldm;
     free_vector(severity,1,maxwav);    double **dnewmp,**doldmp;
     free_imatrix(outcome,1,maxwav+1,1,n);    int i, j, nhstepm, hstepm, h, nstepm ;
     free_vector(moisnais,1,n);    int k;
     free_vector(annais,1,n);    double *xp;
     /* free_matrix(mint,1,maxwav,1,n);    double **gp, **gm;  /* for var eij */
        free_matrix(anint,1,maxwav,1,n);*/    double ***gradg, ***trgradg; /*for var eij */
     free_vector(moisdc,1,n);    double **gradgp, **trgradgp; /* for var p point j */
     free_vector(andc,1,n);    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
        double ***p3mat;
     wav=ivector(1,imx);    double age,agelim, hf;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    double ***mobaverage;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    int theta;
        char digit[4];
     /* Concatenates waves */    char digitp[25];
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
     char fileresprobmorprev[FILENAMELENGTH];
   
       Tcode=ivector(1,100);    if(popbased==1){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      if(mobilav!=0)
       ncodemax[1]=1;        strcpy(digitp,"-populbased-mobilav-");
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      else strcpy(digitp,"-populbased-nomobil-");
          }
    codtab=imatrix(1,100,1,10);    else 
    h=0;      strcpy(digitp,"-stablbased-");
    m=pow(2,cptcoveff);  
      if (mobilav!=0) {
    for(k=1;k<=cptcoveff; k++){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      for(i=1; i <=(m/pow(2,k));i++){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
        for(j=1; j <= ncodemax[k]; j++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
            h++;      }
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    }
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/  
          }    strcpy(fileresprobmorprev,"prmorprev"); 
        }    sprintf(digit,"%-d",ij);
      }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
    }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
       codtab[1][2]=1;codtab[2][2]=2; */    strcat(fileresprobmorprev,fileres);
    /* for(i=1; i <=m ;i++){    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       for(k=1; k <=cptcovn; k++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       }    }
       printf("\n");    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       }   
       scanf("%d",i);*/    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
        pstamp(ficresprobmorprev);
    /* Calculates basic frequencies. Computes observed prevalence at single age    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);
        and prints on file fileres'p'. */    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprobmorprev," p.%-d SE",j);
          for(i=1; i<=nlstate;i++)
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }  
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprobmorprev,"\n");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficgp,"\n# Routine varevsij");
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
          fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     /* For Powell, parameters are in a vector p[] starting at p[1]    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
        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) */    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     if(mle==1){    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    if(popbased==1)
     }      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
        else
     /*--------- results files --------------*/      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     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(ficresvij,"# Age");
      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
    jk=1;        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    fprintf(ficresvij,"\n");
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    xp=vector(1,npar);
    for(i=1,jk=1; i <=nlstate; i++){    dnewm=matrix(1,nlstate,1,npar);
      for(k=1; k <=(nlstate+ndeath); k++){    doldm=matrix(1,nlstate,1,nlstate);
        if (k != i)    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
          {    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
            printf("%d%d ",i,k);  
            fprintf(ficlog,"%d%d ",i,k);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
            fprintf(ficres,"%1d%1d ",i,k);    gpp=vector(nlstate+1,nlstate+ndeath);
            for(j=1; j <=ncovmodel; j++){    gmp=vector(nlstate+1,nlstate+ndeath);
              printf("%f ",p[jk]);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
              fprintf(ficlog,"%f ",p[jk]);    
              fprintf(ficres,"%f ",p[jk]);    if(estepm < stepm){
              jk++;      printf ("Problem %d lower than %d\n",estepm, stepm);
            }    }
            printf("\n");    else  hstepm=estepm;   
            fprintf(ficlog,"\n");    /* For example we decided to compute the life expectancy with the smallest unit */
            fprintf(ficres,"\n");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
          }       nhstepm is the number of hstepm from age to agelim 
      }       nstepm is the number of stepm from age to agelin. 
    }       Look at function hpijx to understand why (it is linked to memory size questions) */
    if(mle==1){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
      /* Computing hessian and covariance matrix */       survival function given by stepm (the optimization length). Unfortunately it
      ftolhess=ftol; /* Usually correct */       means that if the survival funtion is printed every two years of age and if
      hesscov(matcov, p, npar, delti, ftolhess, func);       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.
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    */
    printf("# Scales (for hessian or gradient estimation)\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");    agelim = AGESUP;
    for(i=1,jk=1; i <=nlstate; i++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      for(j=1; j <=nlstate+ndeath; j++){      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
        if (j!=i) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
          fprintf(ficres,"%1d%1d",i,j);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          printf("%1d%1d",i,j);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
          fprintf(ficlog,"%1d%1d",i,j);      gp=matrix(0,nhstepm,1,nlstate);
          for(k=1; k<=ncovmodel;k++){      gm=matrix(0,nhstepm,1,nlstate);
            printf(" %.5e",delti[jk]);  
            fprintf(ficlog," %.5e",delti[jk]);  
            fprintf(ficres," %.5e",delti[jk]);      for(theta=1; theta <=npar; theta++){
            jk++;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
          }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          printf("\n");        }
          fprintf(ficlog,"\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          fprintf(ficres,"\n");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        }  
      }        if (popbased==1) {
    }          if(mobilav ==0){
                for(i=1; i<=nlstate;i++)
    k=1;              prlim[i][i]=probs[(int)age][i][ij];
    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");          }else{ /* mobilav */ 
    if(mle==1)            for(i=1; i<=nlstate;i++)
      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");              prlim[i][i]=mobaverage[(int)age][i][ij];
    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");          }
    for(i=1;i<=npar;i++){        }
      /*  if (k>nlstate) k=1;    
          i1=(i-1)/(ncovmodel*nlstate)+1;        for(j=1; j<= nlstate; j++){
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          for(h=0; h<=nhstepm; h++){
          printf("%s%d%d",alph[k],i1,tab[i]);*/            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
      fprintf(ficres,"%3d",i);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
      if(mle==1)          }
        printf("%3d",i);        }
      fprintf(ficlog,"%3d",i);        /* This for computing probability of death (h=1 means
      for(j=1; j<=i;j++){           computed over hstepm matrices product = hstepm*stepm months) 
        fprintf(ficres," %.5e",matcov[i][j]);           as a weighted average of prlim.
        if(mle==1)        */
          printf(" %.5e",matcov[i][j]);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
        fprintf(ficlog," %.5e",matcov[i][j]);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
      }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
      fprintf(ficres,"\n");        }    
      if(mle==1)        /* end probability of death */
        printf("\n");  
      fprintf(ficlog,"\n");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
      k++;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
    }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
            prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    while((c=getc(ficpar))=='#' && c!= EOF){   
      ungetc(c,ficpar);        if (popbased==1) {
      fgets(line, MAXLINE, ficpar);          if(mobilav ==0){
      puts(line);            for(i=1; i<=nlstate;i++)
      fputs(line,ficparo);              prlim[i][i]=probs[(int)age][i][ij];
    }          }else{ /* mobilav */ 
    ungetc(c,ficpar);            for(i=1; i<=nlstate;i++)
    estepm=0;              prlim[i][i]=mobaverage[(int)age][i][ij];
    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;        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
      fage = agemaxpar;          for(h=0; h<=nhstepm; h++){
    }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                  gm[h][j] += prlim[i][i]*p3mat[i][j][h];
    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);        /* This for computing probability of death (h=1 means
               computed over hstepm matrices product = hstepm*stepm months) 
    while((c=getc(ficpar))=='#' && c!= EOF){           as a weighted average of prlim.
      ungetc(c,ficpar);        */
      fgets(line, MAXLINE, ficpar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
      puts(line);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
      fputs(line,ficparo);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
    }        }    
    ungetc(c,ficpar);        /* end probability of death */
    
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        for(j=1; j<= nlstate; j++) /* vareij */
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          for(h=0; h<=nhstepm; h++){
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
              }
    while((c=getc(ficpar))=='#' && c!= EOF){  
      ungetc(c,ficpar);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
      fgets(line, MAXLINE, ficpar);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
      puts(line);        }
      fputs(line,ficparo);  
    }      } /* End theta */
    ungetc(c,ficpar);  
        trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      for(h=0; h<=nhstepm; h++) /* veij */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
   fscanf(ficpar,"pop_based=%d\n",&popbased);            trgradg[h][j][theta]=gradg[h][theta][j];
   fprintf(ficparo,"pop_based=%d\n",popbased);    
   fprintf(ficres,"pop_based=%d\n",popbased);        for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
          for(theta=1; theta <=npar; theta++)
   while((c=getc(ficpar))=='#' && c!= EOF){          trgradgp[j][theta]=gradgp[theta][j];
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);  
     puts(line);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     fputs(line,ficparo);      for(i=1;i<=nlstate;i++)
   }        for(j=1;j<=nlstate;j++)
   ungetc(c,ficpar);          vareij[i][j][(int)age] =0.;
   
   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);      for(h=0;h<=nhstepm;h++){
 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);        for(k=0;k<=nhstepm;k++){
 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);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
 while((c=getc(ficpar))=='#' && c!= EOF){            for(j=1;j<=nlstate;j++)
     ungetc(c,ficpar);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     fgets(line, MAXLINE, ficpar);        }
     puts(line);      }
     fputs(line,ficparo);    
   }      /* pptj */
   ungetc(c,ficpar);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          varppt[j][i]=doldmp[j][i];
       /* end ppptj */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
 /*------------ gnuplot -------------*/      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   strcpy(optionfilegnuplot,optionfilefiname);   
   strcat(optionfilegnuplot,".gp");      if (popbased==1) {
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        if(mobilav ==0){
     printf("Problem with file %s",optionfilegnuplot);          for(i=1; i<=nlstate;i++)
   }            prlim[i][i]=probs[(int)age][i][ij];
   fclose(ficgp);        }else{ /* mobilav */ 
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);          for(i=1; i<=nlstate;i++)
 /*--------- index.htm --------*/            prlim[i][i]=mobaverage[(int)age][i][ij];
         }
   strcpy(optionfilehtm,optionfile);      }
   strcat(optionfilehtm,".htm");               
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      /* This for computing probability of death (h=1 means
     printf("Problem with %s \n",optionfilehtm), exit(0);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   }         as a weighted average of prlim.
       */
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n      for(j=nlstate+1;j<=nlstate+ndeath;j++){
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
 \n          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
 Total number of observations=%d <br>\n      }    
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      /* end probability of death */
 <hr  size=\"2\" color=\"#EC5E5E\">  
  <ul><li><h4>Parameter files</h4>\n      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
  - Log file of the run: <a href=\"%s\">%s</a><br>\n        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);        for(i=1; i<=nlstate;i++){
   fclose(fichtm);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);      } 
        fprintf(ficresprobmorprev,"\n");
 /*------------ free_vector  -------------*/  
  chdir(path);      fprintf(ficresvij,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
  free_ivector(wav,1,imx);        for(j=1; j<=nlstate;j++){
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          }
  free_ivector(num,1,n);      fprintf(ficresvij,"\n");
  free_vector(agedc,1,n);      free_matrix(gp,0,nhstepm,1,nlstate);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      free_matrix(gm,0,nhstepm,1,nlstate);
  fclose(ficparo);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
  fclose(ficres);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
   /*--------------- Prevalence limit --------------*/    free_vector(gpp,nlstate+1,nlstate+ndeath);
      free_vector(gmp,nlstate+1,nlstate+ndeath);
   strcpy(filerespl,"pl");    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   strcat(filerespl,fileres);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   }  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(ficrespl,"#Prevalence limit\n");    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
   fprintf(ficrespl,"#Age ");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
   fprintf(ficrespl,"\n");    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);
   prlim=matrix(1,nlstate,1,nlstate);    /*  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);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    free_vector(xp,1,npar);
   k=0;    free_matrix(doldm,1,nlstate,1,nlstate);
   agebase=ageminpar;    free_matrix(dnewm,1,nlstate,1,npar);
   agelim=agemaxpar;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   ftolpl=1.e-10;    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   i1=cptcoveff;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (cptcovn < 1){i1=1;}    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
   for(cptcov=1;cptcov<=i1;cptcov++){    fflush(ficgp);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fflush(fichtm); 
         k=k+1;  }  /* end varevsij */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");  /************ Variance of prevlim ******************/
         printf("\n#******");  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[])
         fprintf(ficlog,"\n#******");  {
         for(j=1;j<=cptcoveff;j++) {    /* Variance of prevalence limit */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           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]]);    double **dnewm,**doldm;
         }    int i, j, nhstepm, hstepm;
         fprintf(ficrespl,"******\n");    double *xp;
         printf("******\n");    double *gp, *gm;
         fprintf(ficlog,"******\n");    double **gradg, **trgradg;
            double age,agelim;
         for (age=agebase; age<=agelim; age++){    int theta;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    
           fprintf(ficrespl,"%.0f",age );    pstamp(ficresvpl);
           for(i=1; i<=nlstate;i++)    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
           fprintf(ficrespl," %.5f", prlim[i][i]);    fprintf(ficresvpl,"# Age");
           fprintf(ficrespl,"\n");    for(i=1; i<=nlstate;i++)
         }        fprintf(ficresvpl," %1d-%1d",i,i);
       }    fprintf(ficresvpl,"\n");
     }  
   fclose(ficrespl);    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
   /*------------- h Pij x at various ages ------------*/    doldm=matrix(1,nlstate,1,nlstate);
      
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    hstepm=1*YEARM; /* Every year of age */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    agelim = AGESUP;
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   }      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   printf("Computing pij: result on file '%s' \n", filerespij);      if (stepm >= YEARM) hstepm=1;
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
        gradg=matrix(1,npar,1,nlstate);
   stepsize=(int) (stepm+YEARM-1)/YEARM;      gp=vector(1,nlstate);
   /*if (stepm<=24) stepsize=2;*/      gm=vector(1,nlstate);
   
   agelim=AGESUP;      for(theta=1; theta <=npar; theta++){
   hstepm=stepsize*YEARM; /* Every year of age */        for(i=1; i<=npar; i++){ /* Computes gradient */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
   /* hstepm=1;   aff par mois*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
   k=0;          gp[i] = prlim[i][i];
   for(cptcov=1;cptcov<=i1;cptcov++){      
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(i=1; i<=npar; i++) /* Computes gradient */
       k=k+1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         fprintf(ficrespij,"\n#****** ");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(j=1;j<=cptcoveff;j++)        for(i=1;i<=nlstate;i++)
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          gm[i] = prlim[i][i];
         fprintf(ficrespij,"******\n");  
                for(i=1;i<=nlstate;i++)
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      } /* End theta */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
       trgradg =matrix(1,nlstate,1,npar);
           /*      nhstepm=nhstepm*YEARM; aff par mois*/  
       for(j=1; j<=nlstate;j++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(theta=1; theta <=npar; theta++)
           oldm=oldms;savm=savms;          trgradg[j][theta]=gradg[theta][j];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");      for(i=1;i<=nlstate;i++)
           for(i=1; i<=nlstate;i++)        varpl[i][(int)age] =0.;
             for(j=1; j<=nlstate+ndeath;j++)      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
               fprintf(ficrespij," %1d-%1d",i,j);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           fprintf(ficrespij,"\n");      for(i=1;i<=nlstate;i++)
            for (h=0; h<=nhstepm; h++){        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)      fprintf(ficresvpl,"%.0f ",age );
               for(j=1; j<=nlstate+ndeath;j++)      for(i=1; i<=nlstate;i++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
             fprintf(ficrespij,"\n");      fprintf(ficresvpl,"\n");
              }      free_vector(gp,1,nlstate);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      free_vector(gm,1,nlstate);
           fprintf(ficrespij,"\n");      free_matrix(gradg,1,npar,1,nlstate);
         }      free_matrix(trgradg,1,nlstate,1,npar);
     }    } /* End age */
   }  
     free_vector(xp,1,npar);
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   fclose(ficrespij);  
   }
   
   /*---------- Forecasting ------------------*/  /************ Variance of one-step probabilities  ******************/
   if((stepm == 1) && (strcmp(model,".")==0)){  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[])
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  {
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    int i, j=0,  k1, l1, tj;
   }    int k2, l2, j1,  z1;
   else{    int k=0, l;
     erreur=108;    int first=1, first1, first2;
     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);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     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);    double **dnewm,**doldm;
   }    double *xp;
      double *gp, *gm;
     double **gradg, **trgradg;
   /*---------- Health expectancies and variances ------------*/    double **mu;
     double age, cov[NCOVMAX+1];
   strcpy(filerest,"t");    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   strcat(filerest,fileres);    int theta;
   if((ficrest=fopen(filerest,"w"))==NULL) {    char fileresprob[FILENAMELENGTH];
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    char fileresprobcov[FILENAMELENGTH];
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;    char fileresprobcor[FILENAMELENGTH];
   }    double ***varpij;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);    strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   strcpy(filerese,"e");      printf("Problem with resultfile: %s\n", fileresprob);
   strcat(filerese,fileres);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    strcpy(fileresprobcov,"probcov"); 
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    strcat(fileresprobcov,fileres);
   }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      printf("Problem with resultfile: %s\n", fileresprobcov);
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
   strcpy(fileresv,"v");    strcpy(fileresprobcor,"probcor"); 
   strcat(fileresv,fileres);    strcat(fileresprobcor,fileres);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      printf("Problem with resultfile: %s\n", fileresprobcor);
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   }    }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   calagedate=-1;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    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);
   k=0;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   for(cptcov=1;cptcov<=i1;cptcov++){    pstamp(ficresprob);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       k=k+1;    fprintf(ficresprob,"# Age");
       fprintf(ficrest,"\n#****** ");    pstamp(ficresprobcov);
       for(j=1;j<=cptcoveff;j++)    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresprobcov,"# Age");
       fprintf(ficrest,"******\n");    pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       fprintf(ficreseij,"\n#****** ");    fprintf(ficresprobcor,"# Age");
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");    for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficresvij,"\n#****** ");        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       for(j=1;j<=cptcoveff;j++)        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       fprintf(ficresvij,"******\n");      }  
    /* fprintf(ficresprob,"\n");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fprintf(ficresprobcov,"\n");
       oldm=oldms;savm=savms;    fprintf(ficresprobcor,"\n");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);     */
      xp=vector(1,npar);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       oldm=oldms;savm=savms;    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       if(popbased==1){    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);    first=1;
        }    fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
      fprintf(fichtm,"\n");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
       fprintf(ficrest,"\n");    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
       epj=vector(1,nlstate+1);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
       for(age=bage; age <=fage ;age++){  and drawn. It helps understanding how is the covariance between two incidences.\
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
         if (popbased==1) {    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. \
           for(i=1; i<=nlstate;i++)  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
             prlim[i][i]=probs[(int)age][i][k];  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
         }  standard deviations wide on each axis. <br>\
           Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
         fprintf(ficrest," %4.0f",age);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    cov[1]=1;
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    /* tj=cptcoveff; */
           }    tj = (int) pow(2,cptcoveff);
           epj[nlstate+1] +=epj[j];    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         }    j1=0;
     for(j1=1; j1<=tj;j1++){
         for(i=1, vepp=0.;i <=nlstate;i++)      /*for(i1=1; i1<=ncodemax[t];i1++){ */
           for(j=1;j <=nlstate;j++)      /*j1++;*/
             vepp += vareij[i][j][(int)age];        if  (cptcovn>0) {
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));          fprintf(ficresprob, "\n#********** Variable "); 
         for(j=1;j <=nlstate;j++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));          fprintf(ficresprob, "**********\n#\n");
         }          fprintf(ficresprobcov, "\n#********** Variable "); 
         fprintf(ficrest,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficresprobcov, "**********\n#\n");
     }          
   }          fprintf(ficgp, "\n#********** Variable "); 
 free_matrix(mint,1,maxwav,1,n);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);          fprintf(ficgp, "**********\n#\n");
     free_vector(weight,1,n);          
   fclose(ficreseij);          
   fclose(ficresvij);          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   fclose(ficrest);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   fclose(ficpar);          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   free_vector(epj,1,nlstate+1);          
            fprintf(ficresprobcor, "\n#********** Variable ");    
   /*------- Variance limit prevalence------*/            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
   strcpy(fileresvpl,"vpl");        }
   strcat(fileresvpl,fileres);        
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     exit(0);        gp=vector(1,(nlstate)*(nlstate+ndeath));
   }        gm=vector(1,(nlstate)*(nlstate+ndeath));
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
   k=0;          for (k=1; k<=cptcovn;k++) {
   for(cptcov=1;cptcov<=i1;cptcov++){            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                                                           * 1  1 1 1 1
       k=k+1;                                                           * 2  2 1 1 1
       fprintf(ficresvpl,"\n#****** ");                                                           * 3  1 2 1 1
       for(j=1;j<=cptcoveff;j++)                                                           */
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            /* nbcode[1][1]=0 nbcode[1][2]=1;*/
       fprintf(ficresvpl,"******\n");          }
                for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       varpl=matrix(1,nlstate,(int) bage, (int) fage);          for (k=1; k<=cptcovprod;k++)
       oldm=oldms;savm=savms;            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          
     }      
  }          for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
   fclose(ficresvpl);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
   /*---------- End : free ----------------*/            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            
              k=0;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            for(i=1; i<= (nlstate); i++){
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);              for(j=1; j<=(nlstate+ndeath);j++){
                  k=k+1;
                  gp[k]=pmmij[i][j];
   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);            for(i=1; i<=npar; i++)
                xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   free_matrix(matcov,1,npar,1,npar);      
   free_vector(delti,1,npar);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   free_matrix(agev,1,maxwav,1,imx);            k=0;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);            for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
   fprintf(fichtm,"\n</body>");                k=k+1;
   fclose(fichtm);                gm[k]=pmmij[i][j];
   fclose(ficgp);              }
              }
        
   if(erreur >0){            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     printf("End of Imach with error or warning %d\n",erreur);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);          }
   }else{  
    printf("End of Imach\n");          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
    fprintf(ficlog,"End of Imach\n");            for(theta=1; theta <=npar; theta++)
   }              trgradg[j][theta]=gradg[theta][j];
   printf("See log file on %s\n",filelog);          
   fclose(ficlog);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
    
   /* 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);*/          pmij(pmmij,cov,ncovmodel,x,nlstate);
   /*printf("Total time was %d uSec.\n", total_usecs);*/          
   /*------ End -----------*/          k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
  end:              k=k+1;
 #ifdef windows              mu[k][(int) age]=pmmij[i][j];
   /* chdir(pathcd);*/            }
 #endif          }
  /*system("wgnuplot graph.plt");*/          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
  /*system("../gp37mgw/wgnuplot graph.plt");*/            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
  /*system("cd ../gp37mgw");*/              varpij[i][j][(int)age] = doldm[i][j];
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);          /*printf("\n%d ",(int)age);
  strcat(plotcmd," ");            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
  strcat(plotcmd,optionfilegnuplot);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
  system(plotcmd);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
 #ifdef windows  
   while (z[0] != 'q') {          fprintf(ficresprob,"\n%d ",(int)age);
     /* chdir(path); */          fprintf(ficresprobcov,"\n%d ",(int)age);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");          fprintf(ficresprobcor,"\n%d ",(int)age);
     scanf("%s",z);  
     if (z[0] == 'c') system("./imach");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     else if (z[0] == 'e') system(optionfilehtm);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     else if (z[0] == 'g') system(plotcmd);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     else if (z[0] == 'q') exit(0);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   }            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
 #endif          }
 }          i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } */ /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else        fprintf(ficgp," %%*lf (%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
          else fprintf(ficgp," %%*lf (%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
         }
         else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }
       else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ == *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr = *nberr + 1;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           (*nberr)++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0){
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               }else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
             } /* agedc > 0 */
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           (*nberr)++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   #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"*/
   
   #if defined __INTEL_COMPILER
   #if defined(__GNUC__)
           struct utsname sysInfo;  /* For Intel on Linux and OS/X */
   #endif
   #elif defined(__GNUC__) 
   #ifndef  __APPLE__
   #include <gnu/libc-version.h>  /* Only on gnu */
   #endif
      struct utsname sysInfo;
      int cross = CROSS;
      if (cross){
              printf("Cross-");
              fprintf(ficlog, "Cross-");
      }
   #endif
   
   #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(" for ");fprintf(ficlog," for ");
      
   // 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"); fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #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(" using GNU C version %d.\n", __GNUC_VERSION__);
      fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
      //#ifndef __INTEL_COMPILER 
   #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              fprintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
   int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     int i, j, k, i1 ;
     double ftolpl = 1.e-10;
     double age, agebase, agelim;
   
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
   
       agebase=ageminpar;
       agelim=agemaxpar;
   
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
         //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][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(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
   
           fprintf(ficrespl,"#Age ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
           fprintf(ficrespl,"\n");
           
           for (age=agebase; age<=agelim; age++){
           /* for (age=agebase; age<=agebase; age++){ */
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           } /* Age */
           /* was end of cptcod */
       } /* cptcov */
   }
   
   int hPijx(double *p, int bage, int fage){
       /*------------- h Pij x at various ages ------------*/
   
     int stepsize;
     int agelim;
     int hstepm;
     int nhstepm;
     int h, i, i1, j, k;
   
     double agedeb;
     double ***p3mat;
   
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       i1= pow(2,cptcoveff);
      /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
      /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
      /*   k=k+1;  */
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
         
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
           
           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);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
             fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
         /*}*/
       }
   }
   
   
   /***********************************************/
   /**************** 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 */
       prlim=matrix(1,nlstate,1,nlstate);
       prevalence_limit(p, prlim,  ageminpar, agemaxpar);
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
       /*#include "hpijx.h"*/
       hPijx(p, bage, fage);
       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.1.183


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