Diff for /imach/src/imach.c between versions 1.51 and 1.164

version 1.51, 2002/07/19 12:22:25 version 1.164, 2014/12/16 10:52:11
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.164  2014/12/16 10:52:11  brouard
      Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    * imach.c (Module): Merging 1.61 to 1.162
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.163  2014/12/16 10:30:11  brouard
   case of a health survey which is our main interest) -2- at least a    * imach.c (Module): Merging 1.61 to 1.162
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.162  2014/09/25 11:43:39  brouard
   computed from the time spent in each health state according to a    Summary: temporary backup 0.99!
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.1  2014/09/16 11:06:58  brouard
   simplest model is the multinomial logistic model where pij is the    Summary: With some code (wrong) for nlopt
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Author:
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.161  2014/09/15 20:41:41  brouard
   complex model than "constant and age", you should modify the program    Summary: Problem with macro SQR on Intel compiler
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.160  2014/09/02 09:24:05  brouard
   convergence.    *** empty log message ***
   
   The advantage of this computer programme, compared to a simple    Revision 1.159  2014/09/01 10:34:10  brouard
   multinomial logistic model, is clear when the delay between waves is not    Summary: WIN32
   identical for each individual. Also, if a individual missed an    Author: Brouard
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.158  2014/08/27 17:11:51  brouard
     *** empty log message ***
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.157  2014/08/27 16:26:55  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    Summary: Preparing windows Visual studio version
   states. This elementary transition (by month or quarter trimester,    Author: Brouard
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    In order to compile on Visual studio, time.h is now correct and time_t
   and the contribution of each individual to the likelihood is simply    and tm struct should be used. difftime should be used but sometimes I
   hPijx.    just make the differences in raw time format (time(&now).
     Trying to suppress #ifdef LINUX
   Also this programme outputs the covariance matrix of the parameters but also    Add xdg-open for __linux in order to open default browser.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.156  2014/08/25 20:10:10  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    *** empty log message ***
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.155  2014/08/25 18:32:34  brouard
   from the European Union.    Summary: New compile, minor changes
   It is copyrighted identically to a GNU software product, ie programme and    Author: Brouard
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.154  2014/06/20 17:32:08  brouard
   **********************************************************************/    Summary: Outputs now all graphs of convergence to period prevalence
    
 #include <math.h>    Revision 1.153  2014/06/20 16:45:46  brouard
 #include <stdio.h>    Summary: If 3 live state, convergence to period prevalence on same graph
 #include <stdlib.h>    Author: Brouard
 #include <unistd.h>  
     Revision 1.152  2014/06/18 17:54:09  brouard
 #define MAXLINE 256    Summary: open browser, use gnuplot on same dir than imach if not found in the path
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.151  2014/06/18 16:43:30  brouard
 #define FILENAMELENGTH 80    *** empty log message ***
 /*#define DEBUG*/  
 #define windows    Revision 1.150  2014/06/18 16:42:35  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Author: brouard
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.149  2014/06/18 15:51:14  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Summary: Some fixes in parameter files errors
     Author: Nicolas Brouard
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.148  2014/06/17 17:38:48  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Summary: Nothing new
 #define NCOVMAX 8 /* Maximum number of covariates */    Author: Brouard
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Just a new packaging for OS/X version 0.98nS
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.147  2014/06/16 10:33:11  brouard
 #ifdef windows    *** empty log message ***
 #define DIRSEPARATOR '\\'  
 #define ODIRSEPARATOR '/'    Revision 1.146  2014/06/16 10:20:28  brouard
 #else    Summary: Merge
 #define DIRSEPARATOR '/'    Author: Brouard
 #define ODIRSEPARATOR '\\'  
 #endif    Merge, before building revised version.
   
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    Revision 1.145  2014/06/10 21:23:15  brouard
 int erreur; /* Error number */    Summary: Debugging with valgrind
 int nvar;    Author: Nicolas Brouard
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Lot of changes in order to output the results with some covariates
 int nlstate=2; /* Number of live states */    After the Edimburgh REVES conference 2014, it seems mandatory to
 int ndeath=1; /* Number of dead states */    improve the code.
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    No more memory valgrind error but a lot has to be done in order to
 int popbased=0;    continue the work of splitting the code into subroutines.
     Also, decodemodel has been improved. Tricode is still not
 int *wav; /* Number of waves for this individuual 0 is possible */    optimal. nbcode should be improved. Documentation has been added in
 int maxwav; /* Maxim number of waves */    the source code.
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.143  2014/01/26 09:45:38  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.142  2014/01/26 03:57:36  brouard
 FILE *ficlog;    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *ficresprobmorprev;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 FILE *fichtm; /* Html File */  
 FILE *ficreseij;    Revision 1.141  2014/01/26 02:42:01  brouard
 char filerese[FILENAMELENGTH];    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 FILE  *ficresvij;  
 char fileresv[FILENAMELENGTH];    Revision 1.140  2011/09/02 10:37:54  brouard
 FILE  *ficresvpl;    Summary: times.h is ok with mingw32 now.
 char fileresvpl[FILENAMELENGTH];  
 char title[MAXLINE];    Revision 1.139  2010/06/14 07:50:17  brouard
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    Revision 1.138  2010/04/30 18:19:40  brouard
 char filelog[FILENAMELENGTH]; /* Log file */    *** empty log message ***
 char filerest[FILENAMELENGTH];  
 char fileregp[FILENAMELENGTH];    Revision 1.137  2010/04/29 18:11:38  brouard
 char popfile[FILENAMELENGTH];    (Module): Checking covariates for more complex models
     than V1+V2. A lot of change to be done. Unstable.
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  
     Revision 1.136  2010/04/26 20:30:53  brouard
 #define NR_END 1    (Module): merging some libgsl code. Fixing computation
 #define FREE_ARG char*    of likelione (using inter/intrapolation if mle = 0) in order to
 #define FTOL 1.0e-10    get same likelihood as if mle=1.
     Some cleaning of code and comments added.
 #define NRANSI  
 #define ITMAX 200    Revision 1.135  2009/10/29 15:33:14  brouard
     (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define TOL 2.0e-4  
     Revision 1.134  2009/10/29 13:18:53  brouard
 #define CGOLD 0.3819660    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.133  2009/07/06 10:21:25  brouard
     just nforces
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.132  2009/07/06 08:22:05  brouard
 #define TINY 1.0e-20    Many tings
   
 static double maxarg1,maxarg2;    Revision 1.131  2009/06/20 16:22:47  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Some dimensions resccaled
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.130  2009/05/26 06:44:34  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Module): Max Covariate is now set to 20 instead of 8. A
 #define rint(a) floor(a+0.5)    lot of cleaning with variables initialized to 0. Trying to make
     V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.129  2007/08/31 13:49:27  lievre
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    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 imx;    Revision 1.128  2006/06/30 13:02:05  brouard
 int stepm;    (Module): Clarifications on computing e.j
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.127  2006/04/28 18:11:50  brouard
 int estepm;    (Module): Yes the sum of survivors was wrong since
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
 int m,nb;    (Module): In order to speed up (in case of numerous covariates) we
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    compute health expectancies (without variances) in a first step
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    and then all the health expectancies with variances or standard
 double **pmmij, ***probs, ***mobaverage;    deviation (needs data from the Hessian matrices) which slows the
 double dateintmean=0;    computation.
     In the future we should be able to stop the program is only health
 double *weight;    expectancies and graph are needed without standard deviations.
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.126  2006/04/28 17:23:28  brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    loop. Now we define nhstepma in the age loop.
 double ftolhess; /* Tolerance for computing hessian */    Version 0.98h
   
 /**************** split *************************/    Revision 1.125  2006/04/04 15:20:31  lievre
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Errors in calculation of health expectancies. Age was not initialized.
 {    Forecasting file added.
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.124  2006/03/22 17:13:53  lievre
     Parameters are printed with %lf instead of %f (more numbers after the comma).
    l1 = strlen( path );                 /* length of path */    The log-likelihood is printed in the log file
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    Revision 1.123  2006/03/20 10:52:43  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    * imach.c (Module): <title> changed, corresponds to .htm file
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)    name. <head> headers where missing.
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/  
 #if     defined(__bsd__)                /* get current working directory */    * imach.c (Module): Weights can have a decimal point as for
       extern char       *getwd( );    English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
       if ( getwd( dirc ) == NULL ) {    Modification of warning when the covariates values are not 0 or
 #else    1.
       extern char       *getcwd( );    Version 0.98g
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.122  2006/03/20 09:45:41  brouard
 #endif    (Module): Weights can have a decimal point as for
          return( GLOCK_ERROR_GETCWD );    English (a comma might work with a correct LC_NUMERIC environment,
       }    otherwise the weight is truncated).
       strcpy( name, path );             /* we've got it */    Modification of warning when the covariates values are not 0 or
    } else {                             /* strip direcotry from path */    1.
       s++;                              /* after this, the filename */    Version 0.98g
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.121  2006/03/16 17:45:01  lievre
       strcpy( name, s );                /* save file name */    * imach.c (Module): Comments concerning covariates added
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    * imach.c (Module): refinements in the computation of lli if
    }    status=-2 in order to have more reliable computation if stepm is
    l1 = strlen( dirc );                 /* length of directory */    not 1 month. Version 0.98f
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.120  2006/03/16 15:10:38  lievre
 #else    (Module): refinements in the computation of lli if
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    status=-2 in order to have more reliable computation if stepm is
 #endif    not 1 month. Version 0.98f
    s = strrchr( name, '.' );            /* find last / */  
    s++;    Revision 1.119  2006/03/15 17:42:26  brouard
    strcpy(ext,s);                       /* save extension */    (Module): Bug if status = -2, the loglikelihood was
    l1= strlen( name);    computed as likelihood omitting the logarithm. Version O.98e
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    Revision 1.118  2006/03/14 18:20:07  brouard
    finame[l1-l2]= 0;    (Module): varevsij Comments added explaining the second
    return( 0 );                         /* we're done */    table of variances if popbased=1 .
 }    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
     (Module): Version 0.98d
 /******************************************/  
     Revision 1.117  2006/03/14 17:16:22  brouard
 void replace(char *s, char*t)    (Module): varevsij Comments added explaining the second
 {    table of variances if popbased=1 .
   int i;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   int lg=20;    (Module): Function pstamp added
   i=0;    (Module): Version 0.98d
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.116  2006/03/06 10:29:27  brouard
     (s[i] = t[i]);    (Module): Variance-covariance wrong links and
     if (t[i]== '\\') s[i]='/';    varian-covariance of ej. is needed (Saito).
   }  
 }    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
 int nbocc(char *s, char occ)  
 {    Revision 1.114  2006/02/26 12:57:58  brouard
   int i,j=0;    (Module): Some improvements in processing parameter
   int lg=20;    filename with strsep.
   i=0;  
   lg=strlen(s);    Revision 1.113  2006/02/24 14:20:24  brouard
   for(i=0; i<= lg; i++) {    (Module): Memory leaks checks with valgrind and:
   if  (s[i] == occ ) j++;    datafile was not closed, some imatrix were not freed and on matrix
   }    allocation too.
   return j;  
 }    Revision 1.112  2006/01/30 09:55:26  brouard
     (Module): Back to gnuplot.exe instead of wgnuplot.exe
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.111  2006/01/25 20:38:18  brouard
   /* cuts string t into u and v where u is ended by char occ excluding it    (Module): Lots of cleaning and bugs added (Gompertz)
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    (Module): Comments can be added in data file. Missing date values
      gives u="abcedf" and v="ghi2j" */    can be a simple dot '.'.
   int i,lg,j,p=0;  
   i=0;    Revision 1.110  2006/01/25 00:51:50  brouard
   for(j=0; j<=strlen(t)-1; j++) {    (Module): Lots of cleaning and bugs added (Gompertz)
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Revision 1.109  2006/01/24 19:37:15  brouard
     (Module): Comments (lines starting with a #) are allowed in data.
   lg=strlen(t);  
   for(j=0; j<p; j++) {    Revision 1.108  2006/01/19 18:05:42  lievre
     (u[j] = t[j]);    Gnuplot problem appeared...
   }    To be fixed
      u[p]='\0';  
     Revision 1.107  2006/01/19 16:20:37  brouard
    for(j=0; j<= lg; j++) {    Test existence of gnuplot in imach path
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.106  2006/01/19 13:24:36  brouard
 }    Some cleaning and links added in html output
   
 /********************** nrerror ********************/    Revision 1.105  2006/01/05 20:23:19  lievre
     *** empty log message ***
 void nrerror(char error_text[])  
 {    Revision 1.104  2005/09/30 16:11:43  lievre
   fprintf(stderr,"ERREUR ...\n");    (Module): sump fixed, loop imx fixed, and simplifications.
   fprintf(stderr,"%s\n",error_text);    (Module): If the status is missing at the last wave but we know
   exit(1);    that the person is alive, then we can code his/her status as -2
 }    (instead of missing=-1 in earlier versions) and his/her
 /*********************** vector *******************/    contributions to the likelihood is 1 - Prob of dying from last
 double *vector(int nl, int nh)    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 {    the healthy state at last known wave). Version is 0.98
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Revision 1.103  2005/09/30 15:54:49  lievre
   if (!v) nrerror("allocation failure in vector");    (Module): sump fixed, loop imx fixed, and simplifications.
   return v-nl+NR_END;  
 }    Revision 1.102  2004/09/15 17:31:30  brouard
     Add the possibility to read data file including tab characters.
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.101  2004/09/15 10:38:38  brouard
 {    Fix on curr_time
   free((FREE_ARG)(v+nl-NR_END));  
 }    Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Revision 1.99  2004/06/05 08:57:40  brouard
 {    *** empty log message ***
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Revision 1.98  2004/05/16 15:05:56  brouard
   if (!v) nrerror("allocation failure in ivector");    New version 0.97 . First attempt to estimate force of mortality
   return v-nl+NR_END;    directly from the data i.e. without the need of knowing the health
 }    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
 /******************free ivector **************************/    other analysis, in order to test if the mortality estimated from the
 void free_ivector(int *v, long nl, long nh)    cross-longitudinal survey is different from the mortality estimated
 {    from other sources like vital statistic data.
   free((FREE_ARG)(v+nl-NR_END));  
 }    The same imach parameter file can be used but the option for mle should be -3.
   
 /******************* imatrix *******************************/    Agnès, who wrote this part of the code, tried to keep most of the
 int **imatrix(long nrl, long nrh, long ncl, long nch)    former routines in order to include the new code within the former code.
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    The output is very simple: only an estimate of the intercept and of
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    the slope with 95% confident intervals.
   int **m;  
      Current limitations:
   /* allocate pointers to rows */    A) Even if you enter covariates, i.e. with the
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   if (!m) nrerror("allocation failure 1 in matrix()");    B) There is no computation of Life Expectancy nor Life Table.
   m += NR_END;  
   m -= nrl;    Revision 1.97  2004/02/20 13:25:42  lievre
      Version 0.96d. Population forecasting command line is (temporarily)
      suppressed.
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Revision 1.96  2003/07/15 15:38:55  brouard
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   m[nrl] += NR_END;    rewritten within the same printf. Workaround: many printfs.
   m[nrl] -= ncl;  
      Revision 1.95  2003/07/08 07:54:34  brouard
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    * imach.c (Repository):
      (Repository): Using imachwizard code to output a more meaningful covariance
   /* return pointer to array of pointers to rows */    matrix (cov(a12,c31) instead of numbers.
   return m;  
 }    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    Revision 1.93  2003/06/25 16:33:55  brouard
       int **m;    (Module): On windows (cygwin) function asctime_r doesn't
       long nch,ncl,nrh,nrl;    exist so I changed back to asctime which exists.
      /* free an int matrix allocated by imatrix() */    (Module): Version 0.96b
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    Revision 1.92  2003/06/25 16:30:45  brouard
   free((FREE_ARG) (m+nrl-NR_END));    (Module): On windows (cygwin) function asctime_r doesn't
 }    exist so I changed back to asctime which exists.
   
 /******************* matrix *******************************/    Revision 1.91  2003/06/25 15:30:29  brouard
 double **matrix(long nrl, long nrh, long ncl, long nch)    * imach.c (Repository): Duplicated warning errors corrected.
 {    (Repository): Elapsed time after each iteration is now output. It
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    helps to forecast when convergence will be reached. Elapsed time
   double **m;    is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    Revision 1.90  2003/06/24 12:34:15  brouard
   m += NR_END;    (Module): Some bugs corrected for windows. Also, when
   m -= nrl;    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Revision 1.89  2003/06/24 12:30:52  brouard
   m[nrl] += NR_END;    (Module): Some bugs corrected for windows. Also, when
   m[nrl] -= ncl;    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;    Revision 1.88  2003/06/23 17:54:56  brouard
 }    * 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.
   
 /*************************free matrix ************************/    Revision 1.87  2003/06/18 12:26:01  brouard
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    Version 0.96
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    Revision 1.86  2003/06/17 20:04:08  brouard
   free((FREE_ARG)(m+nrl-NR_END));    (Module): Change position of html and gnuplot routines and added
 }    routine fileappend.
   
 /******************* ma3x *******************************/    Revision 1.85  2003/06/17 13:12:43  brouard
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    * imach.c (Repository): Check when date of death was earlier that
 {    current date of interview. It may happen when the death was just
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    prior to the death. In this case, dh was negative and likelihood
   double ***m;    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    interview.
   if (!m) nrerror("allocation failure 1 in matrix()");    (Repository): Because some people have very long ID (first column)
   m += NR_END;    we changed int to long in num[] and we added a new lvector for
   m -= nrl;    memory allocation. But we also truncated to 8 characters (left
     truncation)
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    (Repository): No more line truncation errors.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.84  2003/06/13 21:44:43  brouard
   m[nrl] -= ncl;    * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    many times. Probs is memory consuming and must be used with
     parcimony.
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;    Revision 1.83  2003/06/10 13:39:11  lievre
   m[nrl][ncl] -= nll;    *** empty log message ***
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;    Revision 1.82  2003/06/05 15:57:20  brouard
      Add log in  imach.c and  fullversion number is now printed.
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  */
     for (j=ncl+1; j<=nch; j++)  /*
       m[i][j]=m[i][j-1]+nlay;     Interpolated Markov Chain
   }  
   return m;    Short summary of the programme:
 }    
     This program computes Healthy Life Expectancies from
 /*************************free ma3x ************************/    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    first survey ("cross") where individuals from different ages are
 {    interviewed on their health status or degree of disability (in the
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    case of a health survey which is our main interest) -2- at least a
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    second wave of interviews ("longitudinal") which measure each change
   free((FREE_ARG)(m+nrl-NR_END));    (if any) in individual health status.  Health expectancies are
 }    computed from the time spent in each health state according to a
     model. More health states you consider, more time is necessary to reach the
 /***************** f1dim *************************/    Maximum Likelihood of the parameters involved in the model.  The
 extern int ncom;    simplest model is the multinomial logistic model where pij is the
 extern double *pcom,*xicom;    probability to be observed in state j at the second wave
 extern double (*nrfunc)(double []);    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
 double f1dim(double x)    '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
   int j;    where the markup *Covariates have to be included here again* invites
   double f;    you to do it.  More covariates you add, slower the
   double *xt;    convergence.
    
   xt=vector(1,ncom);    The advantage of this computer programme, compared to a simple
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    multinomial logistic model, is clear when the delay between waves is not
   f=(*nrfunc)(xt);    identical for each individual. Also, if a individual missed an
   free_vector(xt,1,ncom);    intermediate interview, the information is lost, but taken into
   return f;    account using an interpolation or extrapolation.  
 }  
     hPijx is the probability to be observed in state i at age x+h
 /*****************brent *************************/    conditional to the observed state i at age x. The delay 'h' can be
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    split into an exact number (nh*stepm) of unobserved intermediate
 {    states. This elementary transition (by month, quarter,
   int iter;    semester or year) is modelled as a multinomial logistic.  The hPx
   double a,b,d,etemp;    matrix is simply the matrix product of nh*stepm elementary matrices
   double fu,fv,fw,fx;    and the contribution of each individual to the likelihood is simply
   double ftemp;    hPijx.
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;    Also this programme outputs the covariance matrix of the parameters but also
      of the life expectancies. It also computes the period (stable) prevalence. 
   a=(ax < cx ? ax : cx);    
   b=(ax > cx ? ax : cx);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   x=w=v=bx;             Institut national d'études démographiques, Paris.
   fw=fv=fx=(*f)(x);    This software have been partly granted by Euro-REVES, a concerted action
   for (iter=1;iter<=ITMAX;iter++) {    from the European Union.
     xm=0.5*(a+b);    It is copyrighted identically to a GNU software product, ie programme and
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    software can be distributed freely for non commercial use. Latest version
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    can be accessed at http://euroreves.ined.fr/imach .
     printf(".");fflush(stdout);  
     fprintf(ficlog,".");fflush(ficlog);    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #ifdef DEBUG    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    
     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    **********************************************************************/
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  /*
 #endif    main
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    read parameterfile
       *xmin=x;    read datafile
       return fx;    concatwav
     }    freqsummary
     ftemp=fu;    if (mle >= 1)
     if (fabs(e) > tol1) {      mlikeli
       r=(x-w)*(fx-fv);    print results files
       q=(x-v)*(fx-fw);    if mle==1 
       p=(x-v)*q-(x-w)*r;       computes hessian
       q=2.0*(q-r);    read end of parameter file: agemin, agemax, bage, fage, estepm
       if (q > 0.0) p = -p;        begin-prev-date,...
       q=fabs(q);    open gnuplot file
       etemp=e;    open html file
       e=d;    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
         d=CGOLD*(e=(x >= xm ? a-x : b-x));                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
       else {      freexexit2 possible for memory heap.
         d=p/q;  
         u=x+d;    h Pij x                         | pij_nom  ficrestpij
         if (u-a < tol2 || b-u < tol2)     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
           d=SIGN(tol1,xm-x);         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
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
     }         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
     fu=(*f)(u);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
     if (fu <= fx) {     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)    forecasting if prevfcast==1 prevforecast call prevalence()
         SHFT(fv,fw,fx,fu)    health expectancies
         } else {    Variance-covariance of DFLE
           if (u < x) a=u; else b=u;    prevalence()
           if (fu <= fw || w == x) {     movingaverage()
             v=w;    varevsij() 
             w=u;    if popbased==1 varevsij(,popbased)
             fv=fw;    total life expectancies
             fw=fu;    Variance of period (stable) prevalence
           } else if (fu <= fv || v == x || v == w) {   end
             v=u;  */
             fv=fu;  
           }  
         }  
   }   
   nrerror("Too many iterations in brent");  #include <math.h>
   *xmin=x;  #include <stdio.h>
   return fx;  #include <stdlib.h>
 }  #include <string.h>
   
 /****************** mnbrak ***********************/  #ifdef _WIN32
   #include <io.h>
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #else
             double (*func)(double))  #include <unistd.h>
 {  #endif
   double ulim,u,r,q, dum;  
   double fu;  #include <limits.h>
    #include <sys/types.h>
   *fa=(*func)(*ax);  #include <sys/stat.h>
   *fb=(*func)(*bx);  #include <errno.h>
   if (*fb > *fa) {  /* extern int errno; */
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  /* #ifdef LINUX */
       }  /* #include <time.h> */
   *cx=(*bx)+GOLD*(*bx-*ax);  /* #include "timeval.h" */
   *fc=(*func)(*cx);  /* #else */
   while (*fb > *fc) {  /* #include <sys/time.h> */
     r=(*bx-*ax)*(*fb-*fc);  /* #endif */
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #include <time.h>
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #ifdef GSL
     if ((*bx-u)*(u-*cx) > 0.0) {  #include <gsl/gsl_errno.h>
       fu=(*func)(u);  #include <gsl/gsl_multimin.h>
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #endif
       fu=(*func)(u);  
       if (fu < *fc) {  #ifdef NLOPT
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #include <nlopt.h>
           SHFT(*fb,*fc,fu,(*func)(u))  typedef struct {
           }    double (* function)(double [] );
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  } myfunc_data ;
       u=ulim;  #endif
       fu=(*func)(u);  
     } else {  /* #include <libintl.h> */
       u=(*cx)+GOLD*(*cx-*bx);  /* #define _(String) gettext (String) */
       fu=(*func)(u);  
     }  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)  #define GNUPLOTPROGRAM "gnuplot"
       }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 }  #define FILENAMELENGTH 132
   
 /*************** linmin ************************/  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 int ncom;  
 double *pcom,*xicom;  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
 double (*nrfunc)(double []);  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  #define NINTERVMAX 8
 {  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
   double brent(double ax, double bx, double cx,  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
                double (*f)(double), double tol, double *xmin);  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
   double f1dim(double x);  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  #define MAXN 20000
               double *fc, double (*func)(double));  #define YEARM 12. /**< Number of months per year */
   int j;  #define AGESUP 130
   double xx,xmin,bx,ax;  #define AGEBASE 40
   double fx,fb,fa;  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
    #ifdef _WIN32
   ncom=n;  #define DIRSEPARATOR '\\'
   pcom=vector(1,n);  #define CHARSEPARATOR "\\"
   xicom=vector(1,n);  #define ODIRSEPARATOR '/'
   nrfunc=func;  #else
   for (j=1;j<=n;j++) {  #define DIRSEPARATOR '/'
     pcom[j]=p[j];  #define CHARSEPARATOR "/"
     xicom[j]=xi[j];  #define ODIRSEPARATOR '\\'
   }  #endif
   ax=0.0;  
   xx=1.0;  /* $Id$ */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  /* $State$ */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  char fullversion[]="$Revision$ $Date$"; 
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  char strstart[80];
 #endif  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   for (j=1;j<=n;j++) {  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     xi[j] *= xmin;  int nvar=0, nforce=0; /* Number of variables, number of forces */
     p[j] += xi[j];  /* 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) */
   free_vector(xicom,1,n);  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
   free_vector(pcom,1,n);  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
 }  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   int cptcovprodnoage=0; /**< Number of covariate products without age */   
 /*************** powell ************************/  int cptcoveff=0; /* Total number of covariates to vary for printing results */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  int cptcov=0; /* Working variable */
             double (*func)(double []))  int npar=NPARMAX;
 {  int nlstate=2; /* Number of live states */
   void linmin(double p[], double xi[], int n, double *fret,  int ndeath=1; /* Number of dead states */
               double (*func)(double []));  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int i,ibig,j;  int popbased=0;
   double del,t,*pt,*ptt,*xit;  
   double fp,fptt;  int *wav; /* Number of waves for this individuual 0 is possible */
   double *xits;  int maxwav=0; /* Maxim number of waves */
   pt=vector(1,n);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   ptt=vector(1,n);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   xit=vector(1,n);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   xits=vector(1,n);                     to the likelihood and the sum of weights (done by funcone)*/
   *fret=(*func)(p);  int mle=1, weightopt=0;
   for (j=1;j<=n;j++) pt[j]=p[j];  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   for (*iter=1;;++(*iter)) {  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     fp=(*fret);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     ibig=0;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     del=0.0;  int countcallfunc=0;  /* Count the number of calls to func */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  double jmean=1; /* Mean space between 2 waves */
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  double **matprod2(); /* test */
     for (i=1;i<=n;i++)  double **oldm, **newm, **savm; /* Working pointers to matrices */
       printf(" %d %.12f",i, p[i]);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     fprintf(ficlog," %d %.12f",i, p[i]);  /*FILE *fic ; */ /* Used in readdata only */
     printf("\n");  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     fprintf(ficlog,"\n");  FILE *ficlog, *ficrespow;
     for (i=1;i<=n;i++) {  int globpr=0; /* Global variable for printing or not */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  double fretone; /* Only one call to likelihood */
       fptt=(*fret);  long ipmx=0; /* Number of contributions */
 #ifdef DEBUG  double sw; /* Sum of weights */
       printf("fret=%lf \n",*fret);  char filerespow[FILENAMELENGTH];
       fprintf(ficlog,"fret=%lf \n",*fret);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 #endif  FILE *ficresilk;
       printf("%d",i);fflush(stdout);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       fprintf(ficlog,"%d",i);fflush(ficlog);  FILE *ficresprobmorprev;
       linmin(p,xit,n,fret,func);  FILE *fichtm, *fichtmcov; /* Html File */
       if (fabs(fptt-(*fret)) > del) {  FILE *ficreseij;
         del=fabs(fptt-(*fret));  char filerese[FILENAMELENGTH];
         ibig=i;  FILE *ficresstdeij;
       }  char fileresstde[FILENAMELENGTH];
 #ifdef DEBUG  FILE *ficrescveij;
       printf("%d %.12e",i,(*fret));  char filerescve[FILENAMELENGTH];
       fprintf(ficlog,"%d %.12e",i,(*fret));  FILE  *ficresvij;
       for (j=1;j<=n;j++) {  char fileresv[FILENAMELENGTH];
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  FILE  *ficresvpl;
         printf(" x(%d)=%.12e",j,xit[j]);  char fileresvpl[FILENAMELENGTH];
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  char title[MAXLINE];
       }  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       for(j=1;j<=n;j++) {  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
         printf(" p=%.12e",p[j]);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
         fprintf(ficlog," p=%.12e",p[j]);  char command[FILENAMELENGTH];
       }  int  outcmd=0;
       printf("\n");  
       fprintf(ficlog,"\n");  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #endif  
     }  char filelog[FILENAMELENGTH]; /* Log file */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  char filerest[FILENAMELENGTH];
 #ifdef DEBUG  char fileregp[FILENAMELENGTH];
       int k[2],l;  char popfile[FILENAMELENGTH];
       k[0]=1;  
       k[1]=-1;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       printf("Max: %.12e",(*func)(p));  
       fprintf(ficlog,"Max: %.12e",(*func)(p));  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
       for (j=1;j<=n;j++) {  /* struct timezone tzp; */
         printf(" %.12e",p[j]);  /* extern int gettimeofday(); */
         fprintf(ficlog," %.12e",p[j]);  struct tm tml, *gmtime(), *localtime();
       }  
       printf("\n");  extern time_t time();
       fprintf(ficlog,"\n");  
       for(l=0;l<=1;l++) {  struct tm start_time, end_time, curr_time, last_time, forecast_time;
         for (j=1;j<=n;j++) {  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  struct tm tm;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  char strcurr[80], strfor[80];
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  char *endptr;
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  long lval;
       }  double dval;
 #endif  
   #define NR_END 1
   #define FREE_ARG char*
       free_vector(xit,1,n);  #define FTOL 1.0e-10
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  #define NRANSI 
       free_vector(pt,1,n);  #define ITMAX 200 
       return;  
     }  #define TOL 2.0e-4 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {  #define CGOLD 0.3819660 
       ptt[j]=2.0*p[j]-pt[j];  #define ZEPS 1.0e-10 
       xit[j]=p[j]-pt[j];  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       pt[j]=p[j];  
     }  #define GOLD 1.618034 
     fptt=(*func)(ptt);  #define GLIMIT 100.0 
     if (fptt < fp) {  #define TINY 1.0e-20 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {  static double maxarg1,maxarg2;
         linmin(p,xit,n,fret,func);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
         for (j=1;j<=n;j++) {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
           xi[j][ibig]=xi[j][n];    
           xi[j][n]=xit[j];  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
         }  #define rint(a) floor(a+0.5)
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  static double sqrarg;
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         for(j=1;j<=n;j++){  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
           printf(" %.12e",xit[j]);  int agegomp= AGEGOMP;
           fprintf(ficlog," %.12e",xit[j]);  
         }  int imx; 
         printf("\n");  int stepm=1;
         fprintf(ficlog,"\n");  /* Stepm, step in month: minimum step interpolation*/
 #endif  
       }  int estepm;
     }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   }  
 }  int m,nb;
   long *num;
 /**** Prevalence limit ****************/  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  double **pmmij, ***probs;
 {  double *ageexmed,*agecens;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  double dateintmean=0;
      matrix by transitions matrix until convergence is reached */  
   double *weight;
   int i, ii,j,k;  int **s; /* Status */
   double min, max, maxmin, maxmax,sumnew=0.;  double *agedc;
   double **matprod2();  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
   double **out, cov[NCOVMAX], **pmij();                    * covar=matrix(0,NCOVMAX,1,n); 
   double **newm;                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
   double agefin, delaymax=50 ; /* Max number of years to converge */  double  idx; 
   int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   for (ii=1;ii<=nlstate+ndeath;ii++)  int *Ndum; /** Freq of modality (tricode */
     for (j=1;j<=nlstate+ndeath;j++){  int **codtab; /**< codtab=imatrix(1,100,1,10); */
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
     }  double *lsurv, *lpop, *tpop;
   
    cov[1]=1.;  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
    double ftolhess; /**< Tolerance for computing hessian */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  /**************** split *************************/
     newm=savm;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     /* Covariates have to be included here again */  {
      cov[2]=agefin;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
         the name of the file (name), its extension only (ext) and its first part of the name (finame)
       for (k=1; k<=cptcovn;k++) {    */ 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    char  *ss;                            /* pointer */
         /*      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]]);*/    int   l1, l2;                         /* length counters */
       }  
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    l1 = strlen(path );                   /* length of path */
       for (k=1; k<=cptcovprod;k++)    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so determine current directory */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      strcpy( name, path );               /* we got the fullname name because no directory */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
     savm=oldm;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     oldm=newm;        return( GLOCK_ERROR_GETCWD );
     maxmax=0.;      }
     for(j=1;j<=nlstate;j++){      /* got dirc from getcwd*/
       min=1.;      printf(" DIRC = %s \n",dirc);
       max=0.;    } else {                              /* strip direcotry from path */
       for(i=1; i<=nlstate; i++) {      ss++;                               /* after this, the filename */
         sumnew=0;      l2 = strlen( ss );                  /* length of filename */
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
         prlim[i][j]= newm[i][j]/(1-sumnew);      strcpy( name, ss );         /* save file name */
         max=FMAX(max,prlim[i][j]);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
         min=FMIN(min,prlim[i][j]);      dirc[l1-l2] = 0;                    /* add zero */
       }      printf(" DIRC2 = %s \n",dirc);
       maxmin=max-min;    }
       maxmax=FMAX(maxmax,maxmin);    /* We add a separator at the end of dirc if not exists */
     }    l1 = strlen( dirc );                  /* length of directory */
     if(maxmax < ftolpl){    if( dirc[l1-1] != DIRSEPARATOR ){
       return prlim;      dirc[l1] =  DIRSEPARATOR;
     }      dirc[l1+1] = 0; 
   }      printf(" DIRC3 = %s \n",dirc);
 }    }
     ss = strrchr( name, '.' );            /* find last / */
 /*************** transition probabilities ***************/    if (ss >0){
       ss++;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      strcpy(ext,ss);                     /* save extension */
 {      l1= strlen( name);
   double s1, s2;      l2= strlen(ss)+1;
   /*double t34;*/      strncpy( finame, name, l1-l2);
   int i,j,j1, nc, ii, jj;      finame[l1-l2]= 0;
     }
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){    return( 0 );                          /* we're done */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  }
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  /******************************************/
       }  
       ps[i][j]=s2;  void replace_back_to_slash(char *s, char*t)
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  {
     }    int i;
     for(j=i+1; j<=nlstate+ndeath;j++){    int lg=0;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    i=0;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    lg=strlen(t);
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    for(i=0; i<= lg; i++) {
       }      (s[i] = t[i]);
       ps[i][j]=s2;      if (t[i]== '\\') s[i]='/';
     }    }
   }  }
     /*ps[3][2]=1;*/  
   char *trimbb(char *out, char *in)
   for(i=1; i<= nlstate; i++){  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
      s1=0;    char *s;
     for(j=1; j<i; j++)    s=out;
       s1+=exp(ps[i][j]);    while (*in != '\0'){
     for(j=i+1; j<=nlstate+ndeath; j++)      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
       s1+=exp(ps[i][j]);        in++;
     ps[i][i]=1./(s1+1.);      }
     for(j=1; j<i; j++)      *out++ = *in++;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    }
     for(j=i+1; j<=nlstate+ndeath; j++)    *out='\0';
       ps[i][j]= exp(ps[i][j])*ps[i][i];    return s;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  }
   } /* end i */  
   char *cutl(char *blocc, char *alocc, char *in, char occ)
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  {
     for(jj=1; jj<= nlstate+ndeath; jj++){    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
       ps[ii][jj]=0;       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       ps[ii][ii]=1;       gives blocc="abcdef2ghi" and alocc="j".
     }       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   }    */
     char *s, *t;
     t=in;s=in;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    while ((*in != occ) && (*in != '\0')){
     for(jj=1; jj<= nlstate+ndeath; jj++){      *alocc++ = *in++;
      printf("%lf ",ps[ii][jj]);    }
    }    if( *in == occ){
     printf("\n ");      *(alocc)='\0';
     }      s=++in;
     printf("\n ");printf("%lf ",cov[2]);*/    }
 /*   
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    if (s == t) {/* occ not found */
   goto end;*/      *(alocc-(in-s))='\0';
     return ps;      in=s;
 }    }
     while ( *in != '\0'){
 /**************** Product of 2 matrices ******************/      *blocc++ = *in++;
     }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  
 {    *blocc='\0';
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    return t;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  }
   /* in, b, out are matrice of pointers which should have been initialized  char *cutv(char *blocc, char *alocc, char *in, char occ)
      before: only the contents of out is modified. The function returns  {
      a pointer to pointers identical to out */    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
   long i, j, k;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   for(i=nrl; i<= nrh; i++)       gives blocc="abcdef2ghi" and alocc="j".
     for(k=ncolol; k<=ncoloh; k++)       If occ is not found blocc is null and alocc is equal to in. Returns alocc
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    */
         out[i][k] +=in[i][j]*b[j][k];    char *s, *t;
     t=in;s=in;
   return out;    while (*in != '\0'){
 }      while( *in == occ){
         *blocc++ = *in++;
         s=in;
 /************* Higher Matrix Product ***************/      }
       *blocc++ = *in++;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    }
 {    if (s == t) /* occ not found */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      *(blocc-(in-s))='\0';
      duration (i.e. until    else
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      *(blocc-(in-s)-1)='\0';
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    in=s;
      (typically every 2 years instead of every month which is too big).    while ( *in != '\0'){
      Model is determined by parameters x and covariates have to be      *alocc++ = *in++;
      included manually here.    }
   
      */    *alocc='\0';
     return s;
   int i, j, d, h, k;  }
   double **out, cov[NCOVMAX];  
   double **newm;  int nbocc(char *s, char occ)
   {
   /* Hstepm could be zero and should return the unit matrix */    int i,j=0;
   for (i=1;i<=nlstate+ndeath;i++)    int lg=20;
     for (j=1;j<=nlstate+ndeath;j++){    i=0;
       oldm[i][j]=(i==j ? 1.0 : 0.0);    lg=strlen(s);
       po[i][j][0]=(i==j ? 1.0 : 0.0);    for(i=0; i<= lg; i++) {
     }    if  (s[i] == occ ) j++;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    }
   for(h=1; h <=nhstepm; h++){    return j;
     for(d=1; d <=hstepm; d++){  }
       newm=savm;  
       /* Covariates have to be included here again */  /* void cutv(char *u,char *v, char*t, char occ) */
       cov[1]=1.;  /* { */
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
       for (k=1; k<=cptcovage;k++)  /*      gives u="abcdef2ghi" and v="j" *\/ */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*   int i,lg,j,p=0; */
       for (k=1; k<=cptcovprod;k++)  /*   i=0; */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /*   lg=strlen(t); */
   /*   for(j=0; j<=lg-1; j++) { */
   /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  /*   } */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  /*   for(j=0; j<p; j++) { */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  /*     (u[j] = t[j]); */
       savm=oldm;  /*   } */
       oldm=newm;  /*      u[p]='\0'; */
     }  
     for(i=1; i<=nlstate+ndeath; i++)  /*    for(j=0; j<= lg; j++) { */
       for(j=1;j<=nlstate+ndeath;j++) {  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
         po[i][j][h]=newm[i][j];  /*   } */
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  /* } */
          */  
       }  #ifdef _WIN32
   } /* end h */  char * strsep(char **pp, const char *delim)
   return po;  {
 }    char *p, *q;
            
     if ((p = *pp) == NULL)
 /*************** log-likelihood *************/      return 0;
 double func( double *x)    if ((q = strpbrk (p, delim)) != NULL)
 {    {
   int i, ii, j, k, mi, d, kk;      *pp = q + 1;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      *q = '\0';
   double **out;    }
   double sw; /* Sum of weights */    else
   double lli; /* Individual log likelihood */      *pp = 0;
   long ipmx;    return p;
   /*extern weight */  }
   /* We are differentiating ll according to initial status */  #endif
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)  /********************** nrerror ********************/
     printf(" %d\n",s[4][i]);  
   */  void nrerror(char error_text[])
   cov[1]=1.;  {
     fprintf(stderr,"ERREUR ...\n");
   for(k=1; k<=nlstate; k++) ll[k]=0.;    fprintf(stderr,"%s\n",error_text);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    exit(EXIT_FAILURE);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  }
     for(mi=1; mi<= wav[i]-1; mi++){  /*********************** vector *******************/
       for (ii=1;ii<=nlstate+ndeath;ii++)  double *vector(int nl, int nh)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  {
       for(d=0; d<dh[mi][i]; d++){    double *v;
         newm=savm;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    if (!v) nrerror("allocation failure in vector");
         for (kk=1; kk<=cptcovage;kk++) {    return v-nl+NR_END;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  }
         }  
          /************************ free vector ******************/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  void free_vector(double*v, int nl, int nh)
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  {
         savm=oldm;    free((FREE_ARG)(v+nl-NR_END));
         oldm=newm;  }
          
          /************************ivector *******************************/
       } /* end mult */  int *ivector(long nl,long nh)
        {
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    int *v;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       ipmx +=1;    if (!v) nrerror("allocation failure in ivector");
       sw += weight[i];    return v-nl+NR_END;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  }
     } /* end of wave */  
   } /* end of individual */  /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  {
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    free((FREE_ARG)(v+nl-NR_END));
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  }
   return -l;  
 }  /************************lvector *******************************/
   long *lvector(long nl,long nh)
   {
 /*********** Maximum Likelihood Estimation ***************/    long *v;
     v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    if (!v) nrerror("allocation failure in ivector");
 {    return v-nl+NR_END;
   int i,j, iter;  }
   double **xi,*delti;  
   double fret;  /******************free lvector **************************/
   xi=matrix(1,npar,1,npar);  void free_lvector(long *v, long nl, long nh)
   for (i=1;i<=npar;i++)  {
     for (j=1;j<=npar;j++)    free((FREE_ARG)(v+nl-NR_END));
       xi[i][j]=(i==j ? 1.0 : 0.0);  }
   printf("Powell\n");  fprintf(ficlog,"Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
 }    
     /* allocate pointers to rows */ 
 /**** Computes Hessian and covariance matrix ***/    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    if (!m) nrerror("allocation failure 1 in matrix()"); 
 {    m += NR_END; 
   double  **a,**y,*x,pd;    m -= nrl; 
   double **hess;    
   int i, j,jk;    
   int *indx;    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   double hessii(double p[], double delta, int theta, double delti[]);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   double hessij(double p[], double delti[], int i, int j);    m[nrl] += NR_END; 
   void lubksb(double **a, int npar, int *indx, double b[]) ;    m[nrl] -= ncl; 
   void ludcmp(double **a, int npar, int *indx, double *d) ;    
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   hess=matrix(1,npar,1,npar);    
     /* return pointer to array of pointers to rows */ 
   printf("\nCalculation of the hessian matrix. Wait...\n");    return m; 
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");  } 
   for (i=1;i<=npar;i++){  
     printf("%d",i);fflush(stdout);  /****************** free_imatrix *************************/
     fprintf(ficlog,"%d",i);fflush(ficlog);  void free_imatrix(m,nrl,nrh,ncl,nch)
     hess[i][i]=hessii(p,ftolhess,i,delti);        int **m;
     /*printf(" %f ",p[i]);*/        long nch,ncl,nrh,nrl; 
     /*printf(" %lf ",hess[i][i]);*/       /* free an int matrix allocated by imatrix() */ 
   }  { 
      free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   for (i=1;i<=npar;i++) {    free((FREE_ARG) (m+nrl-NR_END)); 
     for (j=1;j<=npar;j++)  {  } 
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);  /******************* matrix *******************************/
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);  double **matrix(long nrl, long nrh, long ncl, long nch)
         hess[i][j]=hessij(p,delti,i,j);  {
         hess[j][i]=hess[i][j];        long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         /*printf(" %lf ",hess[i][j]);*/    double **m;
       }  
     }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   }    if (!m) nrerror("allocation failure 1 in matrix()");
   printf("\n");    m += NR_END;
   fprintf(ficlog,"\n");    m -= nrl;
   
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      m[nrl] += NR_END;
   a=matrix(1,npar,1,npar);    m[nrl] -= ncl;
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   indx=ivector(1,npar);    return m;
   for (i=1;i<=npar;i++)    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   ludcmp(a,npar,indx,&pd);  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
      */
   for (j=1;j<=npar;j++) {  }
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  /*************************free matrix ************************/
     lubksb(a,npar,indx,x);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     for (i=1;i<=npar;i++){  {
       matcov[i][j]=x[i];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     }    free((FREE_ARG)(m+nrl-NR_END));
   }  }
   
   printf("\n#Hessian matrix#\n");  /******************* ma3x *******************************/
   fprintf(ficlog,"\n#Hessian matrix#\n");  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   for (i=1;i<=npar;i++) {  {
     for (j=1;j<=npar;j++) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       printf("%.3e ",hess[i][j]);    double ***m;
       fprintf(ficlog,"%.3e ",hess[i][j]);  
     }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     printf("\n");    if (!m) nrerror("allocation failure 1 in matrix()");
     fprintf(ficlog,"\n");    m += NR_END;
   }    m -= nrl;
   
   /* Recompute Inverse */    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   for (i=1;i<=npar;i++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    m[nrl] += NR_END;
   ludcmp(a,npar,indx,&pd);    m[nrl] -= ncl;
   
   /*  printf("\n#Hessian matrix recomputed#\n");    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   
   for (j=1;j<=npar;j++) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     for (i=1;i<=npar;i++) x[i]=0;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     x[j]=1;    m[nrl][ncl] += NR_END;
     lubksb(a,npar,indx,x);    m[nrl][ncl] -= nll;
     for (i=1;i<=npar;i++){    for (j=ncl+1; j<=nch; j++) 
       y[i][j]=x[i];      m[nrl][j]=m[nrl][j-1]+nlay;
       printf("%.3e ",y[i][j]);    
       fprintf(ficlog,"%.3e ",y[i][j]);    for (i=nrl+1; i<=nrh; i++) {
     }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     printf("\n");      for (j=ncl+1; j<=nch; j++) 
     fprintf(ficlog,"\n");        m[i][j]=m[i][j-1]+nlay;
   }    }
   */    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   free_matrix(a,1,npar,1,npar);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   free_matrix(y,1,npar,1,npar);    */
   free_vector(x,1,npar);  }
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);  /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   {
 }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
 /*************** hessian matrix ****************/    free((FREE_ARG)(m+nrl-NR_END));
 double hessii( double x[], double delta, int theta, double delti[])  }
 {  
   int i;  /*************** function subdirf ***********/
   int l=1, lmax=20;  char *subdirf(char fileres[])
   double k1,k2;  {
   double p2[NPARMAX+1];    /* Caution optionfilefiname is hidden */
   double res;    strcpy(tmpout,optionfilefiname);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    strcat(tmpout,"/"); /* Add to the right */
   double fx;    strcat(tmpout,fileres);
   int k=0,kmax=10;    return tmpout;
   double l1;  }
   
   fx=func(x);  /*************** function subdirf2 ***********/
   for (i=1;i<=npar;i++) p2[i]=x[i];  char *subdirf2(char fileres[], char *preop)
   for(l=0 ; l <=lmax; l++){  {
     l1=pow(10,l);    
     delts=delt;    /* Caution optionfilefiname is hidden */
     for(k=1 ; k <kmax; k=k+1){    strcpy(tmpout,optionfilefiname);
       delt = delta*(l1*k);    strcat(tmpout,"/");
       p2[theta]=x[theta] +delt;    strcat(tmpout,preop);
       k1=func(p2)-fx;    strcat(tmpout,fileres);
       p2[theta]=x[theta]-delt;    return tmpout;
       k2=func(p2)-fx;  }
       /*res= (k1-2.0*fx+k2)/delt/delt; */  
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  /*************** function subdirf3 ***********/
        char *subdirf3(char fileres[], char *preop, char *preop2)
 #ifdef DEBUG  {
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    
       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);    /* Caution optionfilefiname is hidden */
 #endif    strcpy(tmpout,optionfilefiname);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    strcat(tmpout,"/");
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    strcat(tmpout,preop);
         k=kmax;    strcat(tmpout,preop2);
       }    strcat(tmpout,fileres);
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    return tmpout;
         k=kmax; l=lmax*10.;  }
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  char *asc_diff_time(long time_sec, char ascdiff[])
         delts=delt;  {
       }    long sec_left, days, hours, minutes;
     }    days = (time_sec) / (60*60*24);
   }    sec_left = (time_sec) % (60*60*24);
   delti[theta]=delts;    hours = (sec_left) / (60*60) ;
   return res;    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);  
 double hessij( double x[], double delti[], int thetai,int thetaj)    return ascdiff;
 {  }
   int i;  
   int l=1, l1, lmax=20;  /***************** f1dim *************************/
   double k1,k2,k3,k4,res,fx;  extern int ncom; 
   double p2[NPARMAX+1];  extern double *pcom,*xicom;
   int k;  extern double (*nrfunc)(double []); 
    
   fx=func(x);  double f1dim(double x) 
   for (k=1; k<=2; k++) {  { 
     for (i=1;i<=npar;i++) p2[i]=x[i];    int j; 
     p2[thetai]=x[thetai]+delti[thetai]/k;    double f;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    double *xt; 
     k1=func(p2)-fx;   
      xt=vector(1,ncom); 
     p2[thetai]=x[thetai]+delti[thetai]/k;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    f=(*nrfunc)(xt); 
     k2=func(p2)-fx;    free_vector(xt,1,ncom); 
      return f; 
     p2[thetai]=x[thetai]-delti[thetai]/k;  } 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;  /*****************brent *************************/
    double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     p2[thetai]=x[thetai]-delti[thetai]/k;  { 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    int iter; 
     k4=func(p2)-fx;    double a,b,d,etemp;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    double fu=0,fv,fw,fx;
 #ifdef DEBUG    double ftemp=0.;
     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);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     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);    double e=0.0; 
 #endif   
   }    a=(ax < cx ? ax : cx); 
   return res;    b=(ax > cx ? ax : cx); 
 }    x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
 /************** Inverse of matrix **************/    for (iter=1;iter<=ITMAX;iter++) { 
 void ludcmp(double **a, int n, int *indx, double *d)      xm=0.5*(a+b); 
 {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   int i,imax,j,k;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   double big,dum,sum,temp;      printf(".");fflush(stdout);
   double *vv;      fprintf(ficlog,".");fflush(ficlog);
    #ifdef DEBUGBRENT
   vv=vector(1,n);      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);
   *d=1.0;      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);
   for (i=1;i<=n;i++) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     big=0.0;  #endif
     for (j=1;j<=n;j++)      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       if ((temp=fabs(a[i][j])) > big) big=temp;        *xmin=x; 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        return fx; 
     vv[i]=1.0/big;      } 
   }      ftemp=fu;
   for (j=1;j<=n;j++) {      if (fabs(e) > tol1) { 
     for (i=1;i<j;i++) {        r=(x-w)*(fx-fv); 
       sum=a[i][j];        q=(x-v)*(fx-fw); 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        p=(x-v)*q-(x-w)*r; 
       a[i][j]=sum;        q=2.0*(q-r); 
     }        if (q > 0.0) p = -p; 
     big=0.0;        q=fabs(q); 
     for (i=j;i<=n;i++) {        etemp=e; 
       sum=a[i][j];        e=d; 
       for (k=1;k<j;k++)        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         sum -= a[i][k]*a[k][j];          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       a[i][j]=sum;        else { 
       if ( (dum=vv[i]*fabs(sum)) >= big) {          d=p/q; 
         big=dum;          u=x+d; 
         imax=i;          if (u-a < tol2 || b-u < tol2) 
       }            d=SIGN(tol1,xm-x); 
     }        } 
     if (j != imax) {      } else { 
       for (k=1;k<=n;k++) {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         dum=a[imax][k];      } 
         a[imax][k]=a[j][k];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         a[j][k]=dum;      fu=(*f)(u); 
       }      if (fu <= fx) { 
       *d = -(*d);        if (u >= x) a=x; else b=x; 
       vv[imax]=vv[j];        SHFT(v,w,x,u) 
     }          SHFT(fv,fw,fx,fu) 
     indx[j]=imax;          } else { 
     if (a[j][j] == 0.0) a[j][j]=TINY;            if (u < x) a=u; else b=u; 
     if (j != n) {            if (fu <= fw || w == x) { 
       dum=1.0/(a[j][j]);              v=w; 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;              w=u; 
     }              fv=fw; 
   }              fw=fu; 
   free_vector(vv,1,n);  /* Doesn't work */            } else if (fu <= fv || v == x || v == w) { 
 ;              v=u; 
 }              fv=fu; 
             } 
 void lubksb(double **a, int n, int *indx, double b[])          } 
 {    } 
   int i,ii=0,ip,j;    nrerror("Too many iterations in brent"); 
   double sum;    *xmin=x; 
      return fx; 
   for (i=1;i<=n;i++) {  } 
     ip=indx[i];  
     sum=b[ip];  /****************** mnbrak ***********************/
     b[ip]=b[i];  
     if (ii)  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];              double (*func)(double)) 
     else if (sum) ii=i;  { 
     b[i]=sum;    double ulim,u,r,q, dum;
   }    double fu; 
   for (i=n;i>=1;i--) {   
     sum=b[i];    *fa=(*func)(*ax); 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    *fb=(*func)(*bx); 
     b[i]=sum/a[i][i];    if (*fb > *fa) { 
   }      SHFT(dum,*ax,*bx,dum) 
 }        SHFT(dum,*fb,*fa,dum) 
         } 
 /************ Frequencies ********************/    *cx=(*bx)+GOLD*(*bx-*ax); 
 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)    *fc=(*func)(*cx); 
 {  /* Some frequencies */    while (*fb > *fc) { /* Declining fa, fb, fc */
        r=(*bx-*ax)*(*fb-*fc); 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      q=(*bx-*cx)*(*fb-*fa); 
   int first;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   double ***freq; /* Frequencies */        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
   double *pp;      ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
   double pos, k2, dateintsum=0,k2cpt=0;      if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
   FILE *ficresp;        fu=(*func)(u); 
   char fileresp[FILENAMELENGTH];  #ifdef DEBUG
          /* f(x)=A(x-u)**2+f(u) */
   pp=vector(1,nlstate);        double A, fparabu; 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
   strcpy(fileresp,"p");        fparabu= *fa - A*(*ax-u)*(*ax-u);
   strcat(fileresp,fileres);        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);
   if((ficresp=fopen(fileresp,"w"))==NULL) {        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);
     printf("Problem with prevalence resultfile: %s\n", fileresp);  #endif 
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);      } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
     exit(0);        fu=(*func)(u); 
   }        if (fu < *fc) { 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   j1=0;            SHFT(*fb,*fc,fu,(*func)(u)) 
              } 
   j=cptcoveff;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        u=ulim; 
         fu=(*func)(u); 
   first=1;      } else { 
         u=(*cx)+GOLD*(*cx-*bx); 
   for(k1=1; k1<=j;k1++){        fu=(*func)(u); 
     for(i1=1; i1<=ncodemax[k1];i1++){      } 
       j1++;      SHFT(*ax,*bx,*cx,u) 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        SHFT(*fa,*fb,*fc,fu) 
         scanf("%d", i);*/        } 
       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 ,
       dateintsum=0;  and replaces xi by the actual vector displacement that p was moved. Also returns as fret
       k2cpt=0;  the value of func at the returned location p . This is actually all accomplished by calling the
       for (i=1; i<=imx; i++) {  routines mnbrak and brent .*/
         bool=1;  int ncom; 
         if  (cptcovn>0) {  double *pcom,*xicom;
           for (z1=1; z1<=cptcoveff; z1++)  double (*nrfunc)(double []); 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])   
               bool=0;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         }  { 
         if (bool==1) {    double brent(double ax, double bx, double cx, 
           for(m=firstpass; m<=lastpass; m++){                 double (*f)(double), double tol, double *xmin); 
             k2=anint[m][i]+(mint[m][i]/12.);    double f1dim(double x); 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
               if(agev[m][i]==0) agev[m][i]=agemax+1;                double *fc, double (*func)(double)); 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    int j; 
               if (m<lastpass) {    double xx,xmin,bx,ax; 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double fx,fb,fa;
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];   
               }    ncom=n; 
                  pcom=vector(1,n); 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    xicom=vector(1,n); 
                 dateintsum=dateintsum+k2;    nrfunc=func; 
                 k2cpt++;    for (j=1;j<=n;j++) { 
               }      pcom[j]=p[j]; 
             }      xicom[j]=xi[j]; 
           }    } 
         }    ax=0.0; 
       }    xx=1.0; 
            mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
   #ifdef DEBUG
       if  (cptcovn>0) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         fprintf(ficresp, "\n#********** Variable ");    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  #endif
         fprintf(ficresp, "**********\n#");    for (j=1;j<=n;j++) { 
       }      xi[j] *= xmin; 
       for(i=1; i<=nlstate;i++)      p[j] += xi[j]; 
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    } 
       fprintf(ficresp, "\n");    free_vector(xicom,1,n); 
          free_vector(pcom,1,n); 
       for(i=(int)agemin; i <= (int)agemax+3; i++){  } 
         if(i==(int)agemax+3){  
           fprintf(ficlog,"Total");  
         }else{  /*************** powell ************************/
           if(first==1){  /*
             first=0;  Minimization of a function func of n variables. Input consists of an initial starting point
             printf("See log file for details...\n");  p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
           }  rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
           fprintf(ficlog,"Age %d", i);  such that failure to decrease by more than this amount on one iteration signals doneness. On
         }  output, p is set to the best point found, xi is the then-current direction set, fret is the returned
         for(jk=1; jk <=nlstate ; jk++){  function value at p , and iter is the number of iterations taken. The routine linmin is used.
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)   */
             pp[jk] += freq[jk][m][i];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         }              double (*func)(double [])) 
         for(jk=1; jk <=nlstate ; jk++){  { 
           for(m=-1, pos=0; m <=0 ; m++)    void linmin(double p[], double xi[], int n, double *fret, 
             pos += freq[jk][m][i];                double (*func)(double [])); 
           if(pp[jk]>=1.e-10){    int i,ibig,j; 
             if(first==1){    double del,t,*pt,*ptt,*xit;
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    double fp,fptt;
             }    double *xits;
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    int niterf, itmp;
           }else{  
             if(first==1)    pt=vector(1,n); 
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    ptt=vector(1,n); 
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    xit=vector(1,n); 
           }    xits=vector(1,n); 
         }    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
         for(jk=1; jk <=nlstate ; jk++){      rcurr_time = time(NULL);  
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    for (*iter=1;;++(*iter)) { 
             pp[jk] += freq[jk][m][i];      fp=(*fret); 
         }      ibig=0; 
       del=0.0; 
         for(jk=1,pos=0; jk <=nlstate ; jk++)      rlast_time=rcurr_time;
           pos += pp[jk];      /* (void) gettimeofday(&curr_time,&tzp); */
         for(jk=1; jk <=nlstate ; jk++){      rcurr_time = time(NULL);  
           if(pos>=1.e-5){      curr_time = *localtime(&rcurr_time);
             if(first==1)      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
           }else{     for (i=1;i<=n;i++) {
             if(first==1)        printf(" %d %.12f",i, p[i]);
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        fprintf(ficlog," %d %.12lf",i, p[i]);
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        fprintf(ficrespow," %.12lf", p[i]);
           }      }
           if( i <= (int) agemax){      printf("\n");
             if(pos>=1.e-5){      fprintf(ficlog,"\n");
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      fprintf(ficrespow,"\n");fflush(ficrespow);
               probs[i][jk][j1]= pp[jk]/pos;      if(*iter <=3){
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        tml = *localtime(&rcurr_time);
             }        strcpy(strcurr,asctime(&tml));
             else        rforecast_time=rcurr_time; 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        itmp = strlen(strcurr);
           }        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         }          strcurr[itmp-1]='\0';
                printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
         for(jk=-1; jk <=nlstate+ndeath; jk++)        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
           for(m=-1; m <=nlstate+ndeath; m++)        for(niterf=10;niterf<=30;niterf+=10){
             if(freq[jk][m][i] !=0 ) {          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
             if(first==1)          forecast_time = *localtime(&rforecast_time);
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          strcpy(strfor,asctime(&forecast_time));
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);          itmp = strlen(strfor);
             }          if(strfor[itmp-1]=='\n')
         if(i <= (int) agemax)          strfor[itmp-1]='\0';
           fprintf(ficresp,"\n");          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
         if(first==1)          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
           printf("Others in log...\n");        }
         fprintf(ficlog,"\n");      }
       }      for (i=1;i<=n;i++) { 
     }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   }        fptt=(*fret); 
   dateintmean=dateintsum/k2cpt;  #ifdef DEBUG
              printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
   fclose(ficresp);            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  #endif
   free_vector(pp,1,nlstate);        printf("%d",i);fflush(stdout);
          fprintf(ficlog,"%d",i);fflush(ficlog);
   /* End of Freq */        linmin(p,xit,n,fret,func); 
 }        if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
 /************ Prevalence ********************/          ibig=i; 
 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)        } 
 {  /* Some frequencies */  #ifdef DEBUG
          printf("%d %.12e",i,(*fret));
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        fprintf(ficlog,"%d %.12e",i,(*fret));
   double ***freq; /* Frequencies */        for (j=1;j<=n;j++) {
   double *pp;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   double pos, k2;          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   pp=vector(1,nlstate);        }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=1;j<=n;j++) {
            printf(" p(%d)=%.12e",j,p[j]);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
   j1=0;        }
          printf("\n");
   j=cptcoveff;        fprintf(ficlog,"\n");
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  #endif
        } /* end i */
   for(k1=1; k1<=j;k1++){      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     for(i1=1; i1<=ncodemax[k1];i1++){  #ifdef DEBUG
       j1++;        int k[2],l;
              k[0]=1;
       for (i=-1; i<=nlstate+ndeath; i++)          k[1]=-1;
         for (jk=-1; jk<=nlstate+ndeath; jk++)          printf("Max: %.12e",(*func)(p));
           for(m=agemin; m <= agemax+3; m++)        fprintf(ficlog,"Max: %.12e",(*func)(p));
             freq[i][jk][m]=0;        for (j=1;j<=n;j++) {
                printf(" %.12e",p[j]);
       for (i=1; i<=imx; i++) {          fprintf(ficlog," %.12e",p[j]);
         bool=1;        }
         if  (cptcovn>0) {        printf("\n");
           for (z1=1; z1<=cptcoveff; z1++)        fprintf(ficlog,"\n");
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        for(l=0;l<=1;l++) {
               bool=0;          for (j=1;j<=n;j++) {
         }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         if (bool==1) {            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           for(m=firstpass; m<=lastpass; m++){            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
             k2=anint[m][i]+(mint[m][i]/12.);          }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
               if(agev[m][i]==0) agev[m][i]=agemax+1;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
               if(agev[m][i]==1) agev[m][i]=agemax+2;        }
               if (m<lastpass) {  #endif
                 if (calagedate>0)  
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  
                 else        free_vector(xit,1,n); 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        free_vector(xits,1,n); 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];        free_vector(ptt,1,n); 
               }        free_vector(pt,1,n); 
             }        return; 
           }      } 
         }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       }      for (j=1;j<=n;j++) { /* Computes an extrapolated point */
       for(i=(int)agemin; i <= (int)agemax+3; i++){        ptt[j]=2.0*p[j]-pt[j]; 
         for(jk=1; jk <=nlstate ; jk++){        xit[j]=p[j]-pt[j]; 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        pt[j]=p[j]; 
             pp[jk] += freq[jk][m][i];      } 
         }      fptt=(*func)(ptt); 
         for(jk=1; jk <=nlstate ; jk++){      if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
           for(m=-1, pos=0; m <=0 ; m++)        /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
             pos += freq[jk][m][i];        /* From x1 (P0) distance of x2 is at h and x3 is 2h */
         }        /* Let f"(x2) be the 2nd derivative equal everywhere.  */
                /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
         for(jk=1; jk <=nlstate ; jk++){        /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
             pp[jk] += freq[jk][m][i];        /* Thus we compare delta(2h) with observed f1-f3 */
         }        /* or best gain on one ancient line 'del' with total  */
                /* gain f1-f2 = f1 - f2 - 'del' with del  */
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
          
         for(jk=1; jk <=nlstate ; jk++){            t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
           if( i <= (int) agemax){        t= t- del*SQR(fp-fptt);
             if(pos>=1.e-5){        printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
               probs[i][jk][j1]= pp[jk]/pos;        fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
             }  #ifdef DEBUG
           }        printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
         }/* end jk */               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
       }/* end i */        fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
     } /* end i1 */               (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
   } /* end k1 */        printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
         fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
    #endif
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        if (t < 0.0) { /* Then we use it for last direction */
   free_vector(pp,1,nlstate);          linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
            for (j=1;j<=n;j++) { 
 }  /* End of Freq */            xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
             xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
 /************* Waves Concatenation ***************/          }
           printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
 {  
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  #ifdef DEBUG
      Death is a valid wave (if date is known).          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          for(j=1;j<=n;j++){
      and mw[mi+1][i]. dh depends on stepm.            printf(" %.12e",xit[j]);
      */            fprintf(ficlog," %.12e",xit[j]);
           }
   int i, mi, m;          printf("\n");
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          fprintf(ficlog,"\n");
      double sum=0., jmean=0.;*/  #endif
   int first;        } /* end of t negative */
   int j, k=0,jk, ju, jl;      } /* end if (fptt < fp)  */
   double sum=0.;    } 
   first=0;  } 
   jmin=1e+5;  
   jmax=-1;  /**** Prevalence limit (stable or period prevalence)  ****************/
   jmean=0.;  
   for(i=1; i<=imx; i++){  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     mi=0;  {
     m=firstpass;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     while(s[m][i] <= nlstate){       matrix by transitions matrix until convergence is reached */
       if(s[m][i]>=1)  
         mw[++mi][i]=m;    int i, ii,j,k;
       if(m >=lastpass)    double min, max, maxmin, maxmax,sumnew=0.;
         break;    /* double **matprod2(); */ /* test */
       else    double **out, cov[NCOVMAX+1], **pmij();
         m++;    double **newm;
     }/* end while */    double agefin, delaymax=50 ; /* Max number of years to converge */
     if (s[m][i] > nlstate){  
       mi++;     /* Death is another wave */    for (ii=1;ii<=nlstate+ndeath;ii++)
       /* if(mi==0)  never been interviewed correctly before death */      for (j=1;j<=nlstate+ndeath;j++){
          /* Only death is a correct wave */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       mw[mi][i]=m;      }
     }  
      cov[1]=1.;
     wav[i]=mi;   
     if(mi==0){   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       if(first==0){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);      newm=savm;
         first=1;      /* Covariates have to be included here again */
       }      cov[2]=agefin;
       if(first==1){      
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);      for (k=1; k<=cptcovn;k++) {
       }        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     } /* end mi==0 */        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
   }      }
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   for(i=1; i<=imx; i++){      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
     for(mi=1; mi<wav[i];mi++){      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
       if (stepm <=0)      
         dh[mi][i]=1;      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       else{      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         if (s[mw[mi+1][i]][i] > nlstate) {      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
           if (agedc[i] < 2*AGESUP) {      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
           if(j==0) j=1;  /* Survives at least one month after exam */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
           k=k+1;      
           if (j >= jmax) jmax=j;      savm=oldm;
           if (j <= jmin) jmin=j;      oldm=newm;
           sum=sum+j;      maxmax=0.;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      for(j=1;j<=nlstate;j++){
           }        min=1.;
         }        max=0.;
         else{        for(i=1; i<=nlstate; i++) {
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          sumnew=0;
           k=k+1;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           if (j >= jmax) jmax=j;          prlim[i][j]= newm[i][j]/(1-sumnew);
           else if (j <= jmin)jmin=j;          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          max=FMAX(max,prlim[i][j]);
           sum=sum+j;          min=FMIN(min,prlim[i][j]);
         }        }
         jk= j/stepm;        maxmin=max-min;
         jl= j -jk*stepm;        maxmax=FMAX(maxmax,maxmin);
         ju= j -(jk+1)*stepm;      }
         if(jl <= -ju)      if(maxmax < ftolpl){
           dh[mi][i]=jk;        return prlim;
         else      }
           dh[mi][i]=jk+1;    }
         if(dh[mi][i]==0)  }
           dh[mi][i]=1; /* At least one step */  
       }  /*************** transition probabilities ***************/ 
     }  
   }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   jmean=sum/k;  {
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    /* According to parameters values stored in x and the covariate's values stored in cov,
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);       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]
 /*********** Tricode ****************************/       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
 void tricode(int *Tvar, int **nbcode, int imx)       ncth covariate in the global vector x is given by the formula:
 {       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
   int Ndum[20],ij=1, k, j, i;       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
   int cptcode=0;       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
   cptcoveff=0;       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
         Outputs ps[i][j] the probability to be observed in j being in j according to
   for (k=0; k<19; k++) Ndum[k]=0;       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   for (k=1; k<=7; k++) ncodemax[k]=0;    */
     double s1, lnpijopii;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    /*double t34;*/
     for (i=1; i<=imx; i++) {    int i,j, nc, ii, jj;
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;      for(i=1; i<= nlstate; i++){
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        for(j=1; j<i;j++){
       if (ij > cptcode) cptcode=ij;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     }            /*lnpijopii += param[i][j][nc]*cov[nc];*/
             lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
     for (i=0; i<=cptcode; i++) {  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       if(Ndum[i]!=0) ncodemax[j]++;          }
     }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     ij=1;  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         }
         for(j=i+1; j<=nlstate+ndeath;j++){
     for (i=1; i<=ncodemax[j]; i++) {          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       for (k=0; k<=19; k++) {            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
         if (Ndum[k] != 0) {            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
           nbcode[Tvar[j]][ij]=k;  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
                    }
           ij++;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         }        }
         if (ij > ncodemax[j]) break;      }
       }        
     }      for(i=1; i<= nlstate; i++){
   }          s1=0;
         for(j=1; j<i; j++){
  for (k=0; k<19; k++) Ndum[k]=0;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
  for (i=1; i<=ncovmodel-2; i++) {        }
    ij=Tvar[i];        for(j=i+1; j<=nlstate+ndeath; j++){
    Ndum[ij]++;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
  }          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         }
  ij=1;        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
  for (i=1; i<=10; i++) {        ps[i][i]=1./(s1+1.);
    if((Ndum[i]!=0) && (i<=ncovcol)){        /* Computing other pijs */
      Tvaraff[ij]=i;        for(j=1; j<i; j++)
      ij++;          ps[i][j]= exp(ps[i][j])*ps[i][i];
    }        for(j=i+1; j<=nlstate+ndeath; j++)
  }          ps[i][j]= exp(ps[i][j])*ps[i][i];
          /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
  cptcoveff=ij-1;      } /* end i */
 }      
       for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
 /*********** Health Expectancies ****************/        for(jj=1; jj<= nlstate+ndeath; jj++){
           ps[ii][jj]=0;
 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 )          ps[ii][ii]=1;
         }
 {      }
   /* Health expectancies */      
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;      
   double age, agelim, hf;      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
   double ***p3mat,***varhe;      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   double **dnewm,**doldm;      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
   double *xp;      /*   } */
   double **gp, **gm;      /*   printf("\n "); */
   double ***gradg, ***trgradg;      /* } */
   int theta;      /* printf("\n ");printf("%lf ",cov[2]);*/
       /*
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   xp=vector(1,npar);        goto end;*/
   dnewm=matrix(1,nlstate*2,1,npar);      return ps;
   doldm=matrix(1,nlstate*2,1,nlstate*2);  }
    
   fprintf(ficreseij,"# Health expectancies\n");  /**************** Product of 2 matrices ******************/
   fprintf(ficreseij,"# Age");  
   for(i=1; i<=nlstate;i++)  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
     for(j=1; j<=nlstate;j++)  {
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   fprintf(ficreseij,"\n");       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
   if(estepm < stepm){       before: only the contents of out is modified. The function returns
     printf ("Problem %d lower than %d\n",estepm, stepm);       a pointer to pointers identical to out */
   }    int i, j, k;
   else  hstepm=estepm;      for(i=nrl; i<= nrh; i++)
   /* We compute the life expectancy from trapezoids spaced every estepm months      for(k=ncolol; k<=ncoloh; k++){
    * This is mainly to measure the difference between two models: for example        out[i][k]=0.;
    * if stepm=24 months pijx are given only every 2 years and by summing them        for(j=ncl; j<=nch; j++)
    * we are calculating an estimate of the Life Expectancy assuming a linear          out[i][k] +=in[i][j]*b[j][k];
    * progression inbetween and thus overestimating or underestimating according      }
    * to the curvature of the survival function. If, for the same date, we    return out;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  }
    * to compare the new estimate of Life expectancy with the same linear  
    * hypothesis. A more precise result, taking into account a more precise  
    * curvature will be obtained if estepm is as small as stepm. */  /************* Higher Matrix Product ***************/
   
   /* For example we decided to compute the life expectancy with the smallest unit */  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   /* 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    /* Computes the transition matrix starting at age 'age' over 
      nstepm is the number of stepm from age to agelin.       'nhstepm*hstepm*stepm' months (i.e. until
      Look at hpijx to understand the reason of that which relies in memory size       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
      and note for a fixed period like estepm months */       nhstepm*hstepm matrices. 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
      survival function given by stepm (the optimization length). Unfortunately it       (typically every 2 years instead of every month which is too big 
      means that if the survival funtion is printed only each two years of age and if       for the memory).
      you sum them up and add 1 year (area under the trapezoids) you won't get the same       Model is determined by parameters x and covariates have to be 
      results. So we changed our mind and took the option of the best precision.       included manually here. 
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */       */
   
   agelim=AGESUP;    int i, j, d, h, k;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double **out, cov[NCOVMAX+1];
     /* nhstepm age range expressed in number of stepm */    double **newm;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    /* Hstepm could be zero and should return the unit matrix */
     /* if (stepm >= YEARM) hstepm=1;*/    for (i=1;i<=nlstate+ndeath;i++)
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      for (j=1;j<=nlstate+ndeath;j++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        oldm[i][j]=(i==j ? 1.0 : 0.0);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);        po[i][j][0]=(i==j ? 1.0 : 0.0);
     gp=matrix(0,nhstepm,1,nlstate*2);      }
     gm=matrix(0,nhstepm,1,nlstate*2);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      for(d=1; d <=hstepm; d++){
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        newm=savm;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          /* Covariates have to be included here again */
          cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        for (k=1; k<=cptcovn;k++) 
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     /* Computing Variances of health expectancies */        for (k=1; k<=cptcovage;k++)
           cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      for(theta=1; theta <=npar; theta++){        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
       for(i=1; i<=npar; i++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
          /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       cptj=0;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       for(j=1; j<= nlstate; j++){                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(i=1; i<=nlstate; i++){        savm=oldm;
           cptj=cptj+1;        oldm=newm;
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      }
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      for(i=1; i<=nlstate+ndeath; i++)
           }        for(j=1;j<=nlstate+ndeath;j++) {
         }          po[i][j][h]=newm[i][j];
       }          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
              }
            /*printf("h=%d ",h);*/
       for(i=1; i<=npar; i++)    } /* end h */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  /*     printf("\n H=%d \n",h); */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      return po;
        }
       cptj=0;  
       for(j=1; j<= nlstate; j++){  #ifdef NLOPT
         for(i=1;i<=nlstate;i++){    double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
           cptj=cptj+1;    double fret;
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    double *xt;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    int j;
           }    myfunc_data *d2 = (myfunc_data *) pd;
         }  /* xt = (p1-1); */
       }    xt=vector(1,n); 
       for(j=1; j<= nlstate*2; j++)    for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
         for(h=0; h<=nhstepm-1; h++){  
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
         }    /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
      }    printf("Function = %.12lf ",fret);
        for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
 /* End theta */    printf("\n");
    free_vector(xt,1,n);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    return fret;
   }
      for(h=0; h<=nhstepm-1; h++)  #endif
       for(j=1; j<=nlstate*2;j++)  
         for(theta=1; theta <=npar; theta++)  /*************** log-likelihood *************/
           trgradg[h][j][theta]=gradg[h][theta][j];  double func( double *x)
        {
     int i, ii, j, k, mi, d, kk;
      for(i=1;i<=nlstate*2;i++)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       for(j=1;j<=nlstate*2;j++)    double **out;
         varhe[i][j][(int)age] =0.;    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
      printf("%d|",(int)age);fflush(stdout);    int s1, s2;
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);    double bbh, survp;
      for(h=0;h<=nhstepm-1;h++){    long ipmx;
       for(k=0;k<=nhstepm-1;k++){    /*extern weight */
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    /* We are differentiating ll according to initial status */
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         for(i=1;i<=nlstate*2;i++)    /*for(i=1;i<imx;i++) 
           for(j=1;j<=nlstate*2;j++)      printf(" %d\n",s[4][i]);
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    */
       }  
     }    ++countcallfunc;
     /* Computing expectancies */  
     for(i=1; i<=nlstate;i++)    cov[1]=1.;
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  
              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]);*/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         /* Computes the values of the ncovmodel covariates of the model
         }           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
     fprintf(ficreseij,"%3.0f",age );           to be observed in j being in i according to the model.
     cptj=0;         */
     for(i=1; i<=nlstate;i++)        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
       for(j=1; j<=nlstate;j++){          cov[2+k]=covar[Tvar[k]][i];
         cptj++;        }
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
       }           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
     fprintf(ficreseij,"\n");           has been calculated etc */
            for(mi=1; mi<= wav[i]-1; mi++){
     free_matrix(gm,0,nhstepm,1,nlstate*2);          for (ii=1;ii<=nlstate+ndeath;ii++)
     free_matrix(gp,0,nhstepm,1,nlstate*2);            for (j=1;j<=nlstate+ndeath;j++){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
   }          for(d=0; d<dh[mi][i]; d++){
   printf("\n");            newm=savm;
   fprintf(ficlog,"\n");            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]; /* Tage[kk] gives the data-covariate associated with age */
   free_matrix(dnewm,1,nlstate*2,1,npar);            }
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
             oldm=newm;
 /************ Variance ******************/          } /* end mult */
 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)        
 {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   /* Variance of health expectancies */          /* But now since version 0.9 we anticipate for bias at large stepm.
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   /* double **newm;*/           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double **dnewm,**doldm;           * the nearest (and in case of equal distance, to the lowest) interval but now
   double **dnewmp,**doldmp;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   int i, j, nhstepm, hstepm, h, nstepm ;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   int k, cptcode;           * probability in order to take into account the bias as a fraction of the way
   double *xp;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   double **gp, **gm;  /* for var eij */           * -stepm/2 to stepm/2 .
   double ***gradg, ***trgradg; /*for var eij */           * For stepm=1 the results are the same as for previous versions of Imach.
   double **gradgp, **trgradgp; /* for var p point j */           * For stepm > 1 the results are less biased than in previous versions. 
   double *gpp, *gmp; /* for var p point j */           */
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */          s1=s[mw[mi][i]][i];
   double ***p3mat;          s2=s[mw[mi+1][i]][i];
   double age,agelim, hf;          bbh=(double)bh[mi][i]/(double)stepm; 
   int theta;          /* bias bh is positive if real duration
   char digit[4];           * is higher than the multiple of stepm and negative otherwise.
   char digitp[16];           */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   char fileresprobmorprev[FILENAMELENGTH];          if( s2 > nlstate){ 
             /* i.e. if s2 is a death state and if the date of death is known 
   if(popbased==1)               then the contribution to the likelihood is the probability to 
     strcpy(digitp,"-populbased-");               die between last step unit time and current  step unit time, 
   else               which is also equal to probability to die before dh 
     strcpy(digitp,"-stablbased-");               minus probability to die before dh-stepm . 
                In version up to 0.92 likelihood was computed
   strcpy(fileresprobmorprev,"prmorprev");          as if date of death was unknown. Death was treated as any other
   sprintf(digit,"%-d",ij);          health state: the date of the interview describes the actual state
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/          and not the date of a change in health state. The former idea was
   strcat(fileresprobmorprev,digit); /* Tvar to be done */          to consider that at each interview the state was recorded
   strcat(fileresprobmorprev,digitp); /* Popbased or not */          (healthy, disable or death) and IMaCh was corrected; but when we
   strcat(fileresprobmorprev,fileres);          introduced the exact date of death then we should have modified
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {          the contribution of an exact death to the likelihood. This new
     printf("Problem with resultfile: %s\n", fileresprobmorprev);          contribution is smaller and very dependent of the step unit
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);          stepm. It is no more the probability to die between last interview
   }          and month of death but the probability to survive from last
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);          interview up to one month before death multiplied by the
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);          probability to die within a month. Thanks to Chris
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");          Jackson for correcting this bug.  Former versions increased
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);          mortality artificially. The bad side is that we add another loop
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){          which slows down the processing. The difference can be up to 10%
     fprintf(ficresprobmorprev," p.%-d SE",j);          lower mortality.
     for(i=1; i<=nlstate;i++)            */
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);            lli=log(out[s1][s2] - savm[s1][s2]);
   }    
   fprintf(ficresprobmorprev,"\n");  
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {          } else if  (s2==-2) {
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);            for (j=1,survp=0. ; j<=nlstate; j++) 
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     exit(0);            /*survp += out[s1][j]; */
   }            lli= log(survp);
   else{          }
     fprintf(ficgp,"\n# Routine varevsij");          
   }          else if  (s2==-4) { 
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {            for (j=3,survp=0. ; j<=nlstate; j++)  
     printf("Problem with html file: %s\n", optionfilehtm);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);            lli= log(survp); 
     exit(0);          } 
   }  
   else{          else if  (s2==-5) { 
     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");            for (j=1,survp=0. ; j<=2; j++)  
   }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);            lli= log(survp); 
           } 
   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");          
   fprintf(ficresvij,"# Age");          else{
   for(i=1; i<=nlstate;i++)            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     for(j=1; j<=nlstate;j++)            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          } 
   fprintf(ficresvij,"\n");          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
   xp=vector(1,npar);          /*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); */
   dnewm=matrix(1,nlstate,1,npar);          ipmx +=1;
   doldm=matrix(1,nlstate,1,nlstate);          sw += weight[i];
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        } /* end of wave */
       } /* end of individual */
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);    }  else if(mle==2){
   gpp=vector(nlstate+1,nlstate+ndeath);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   gmp=vector(nlstate+1,nlstate+ndeath);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   if(estepm < stepm){            for (j=1;j<=nlstate+ndeath;j++){
     printf ("Problem %d lower than %d\n",estepm, stepm);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   else  hstepm=estepm;              }
   /* For example we decided to compute the life expectancy with the smallest unit */          for(d=0; d<=dh[mi][i]; d++){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.            newm=savm;
      nhstepm is the number of hstepm from age to agelim            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      nstepm is the number of stepm from age to agelin.            for (kk=1; kk<=cptcovage;kk++) {
      Look at hpijx to understand the reason of that which relies in memory size              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      and note for a fixed period like k years */            }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      survival function given by stepm (the optimization length). Unfortunately it                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      means that if the survival funtion is printed only each two years of age and if            savm=oldm;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            oldm=newm;
      results. So we changed our mind and took the option of the best precision.          } /* end mult */
   */        
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          s1=s[mw[mi][i]][i];
   agelim = AGESUP;          s2=s[mw[mi+1][i]][i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          bbh=(double)bh[mi][i]/(double)stepm; 
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          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 = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          ipmx +=1;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          sw += weight[i];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     gp=matrix(0,nhstepm,1,nlstate);        } /* end of wave */
     gm=matrix(0,nhstepm,1,nlstate);      } /* end of individual */
     }  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++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
       if (popbased==1) {          for(d=0; d<dh[mi][i]; d++){
         for(i=1; i<=nlstate;i++)            newm=savm;
           prlim[i][i]=probs[(int)age][i][ij];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(j=1; j<= nlstate; j++){            }
         for(h=0; h<=nhstepm; h++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            savm=oldm;
         }            oldm=newm;
       }          } /* end mult */
       /* This for computing forces of mortality (h=1)as a weighted average */        
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){          s1=s[mw[mi][i]][i];
         for(i=1; i<= nlstate; i++)          s2=s[mw[mi+1][i]][i];
           gpp[j] += prlim[i][i]*p3mat[i][j][1];          bbh=(double)bh[mi][i]/(double)stepm; 
       }              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 */
       /* end force of mortality */          ipmx +=1;
           sw += weight[i];
       for(i=1; i<=npar; i++) /* Computes gradient */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        } /* end of wave */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        } /* end of individual */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       if (popbased==1) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(i=1; i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
           prlim[i][i]=probs[(int)age][i][ij];          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<= nlstate; j++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(h=0; h<=nhstepm; h++){            }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          for(d=0; d<dh[mi][i]; d++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
       /* This for computing force of mortality (h=1)as a weighted average */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){            }
         for(i=1; i<= nlstate; i++)          
           gmp[j] += prlim[i][i]*p3mat[i][j][1];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                             1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       /* end force of mortality */            savm=oldm;
             oldm=newm;
       for(j=1; j<= nlstate; j++) /* vareij */          } /* end mult */
         for(h=0; h<=nhstepm; h++){        
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */          if( s2 > nlstate){ 
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];            lli=log(out[s1][s2] - savm[s1][s2]);
       }          }else{
             lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     } /* End theta */          }
           ipmx +=1;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(h=0; h<=nhstepm; h++) /* veij */  /*      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(j=1; j<=nlstate;j++)        } /* end of wave */
         for(theta=1; theta <=npar; theta++)      } /* end of individual */
           trgradg[h][j][theta]=gradg[h][theta][j];    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(theta=1; theta <=npar; theta++)        for(mi=1; mi<= wav[i]-1; mi++){
         trgradgp[j][theta]=gradgp[theta][j];          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1;i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1;j<=nlstate;j++)            }
         vareij[i][j][(int)age] =0.;          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     for(h=0;h<=nhstepm;h++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(k=0;k<=nhstepm;k++){            for (kk=1; kk<=cptcovage;kk++) {
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            }
         for(i=1;i<=nlstate;i++)          
           for(j=1;j<=nlstate;j++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
     }            oldm=newm;
           } /* end mult */
     /* pptj */        
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);          s1=s[mw[mi][i]][i];
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);          s2=s[mw[mi+1][i]][i];
     for(j=nlstate+1;j<=nlstate+ndeath;j++)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       for(i=nlstate+1;i<=nlstate+ndeath;i++)          ipmx +=1;
         varppt[j][i]=doldmp[j][i];          sw += weight[i];
     /* end ppptj */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);            /*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]);*/
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);        } /* end of wave */
        } /* end of individual */
     if (popbased==1) {    } /* End of if */
       for(i=1; i<=nlstate;i++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         prlim[i][i]=probs[(int)age][i][ij];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
        return -l;
     /* This for computing force of mortality (h=1)as a weighted average */  }
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){  
       for(i=1; i<= nlstate; i++)  /*************** log-likelihood *************/
         gmp[j] += prlim[i][i]*p3mat[i][j][1];  double funcone( double *x)
     }      {
     /* end force of mortality */    /* Same as likeli but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){    double **out;
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));    double lli; /* Individual log likelihood */
       for(i=1; i<=nlstate;i++){    double llt;
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);    int s1, s2;
       }    double bbh, survp;
     }    /*extern weight */
     fprintf(ficresprobmorprev,"\n");    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     fprintf(ficresvij,"%.0f ",age );    /*for(i=1;i<imx;i++) 
     for(i=1; i<=nlstate;i++)      printf(" %d\n",s[4][i]);
       for(j=1; j<=nlstate;j++){    */
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    cov[1]=1.;
       }  
     fprintf(ficresvij,"\n");    for(k=1; k<=nlstate; k++) ll[k]=0.;
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      for(mi=1; mi<= wav[i]-1; mi++){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (ii=1;ii<=nlstate+ndeath;ii++)
   } /* End age */          for (j=1;j<=nlstate+ndeath;j++){
   free_vector(gpp,nlstate+1,nlstate+ndeath);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(gmp,nlstate+1,nlstate+ndeath);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);          }
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/        for(d=0; d<dh[mi][i]; d++){
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");          newm=savm;
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");          for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);          }
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   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);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
           /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
   free_vector(xp,1,npar);          savm=oldm;
   free_matrix(doldm,1,nlstate,1,nlstate);          oldm=newm;
   free_matrix(dnewm,1,nlstate,1,npar);        } /* end mult */
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);        s1=s[mw[mi][i]][i];
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        s2=s[mw[mi+1][i]][i];
   fclose(ficresprobmorprev);        bbh=(double)bh[mi][i]/(double)stepm; 
   fclose(ficgp);        /* bias is positive if real duration
   fclose(fichtm);         * is higher than the multiple of stepm and negative otherwise.
          */
 }        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
 /************ Variance of prevlim ******************/        } else if  (s2==-2) {
 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)          for (j=1,survp=0. ; j<=nlstate; j++) 
 {            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   /* Variance of prevalence limit */          lli= log(survp);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        }else if (mle==1){
   double **newm;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double **dnewm,**doldm;        } else if(mle==2){
   int i, j, nhstepm, hstepm;          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 */
   int k, cptcode;        } else if(mle==3){  /* exponential inter-extrapolation */
   double *xp;          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 */
   double *gp, *gm;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   double **gradg, **trgradg;          lli=log(out[s1][s2]); /* Original formula */
   double age,agelim;        } else{  /* mle=0 back to 1 */
   int theta;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
              /*lli=log(out[s1][s2]); */ /* Original formula */
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");        } /* End of if */
   fprintf(ficresvpl,"# Age");        ipmx +=1;
   for(i=1; i<=nlstate;i++)        sw += weight[i];
       fprintf(ficresvpl," %1d-%1d",i,i);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fprintf(ficresvpl,"\n");        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         if(globpr){
   xp=vector(1,npar);          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   dnewm=matrix(1,nlstate,1,npar);   %11.6f %11.6f %11.6f ", \
   doldm=matrix(1,nlstate,1,nlstate);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                    2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   hstepm=1*YEARM; /* Every year of age */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            llt +=ll[k]*gipmx/gsw;
   agelim = AGESUP;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          fprintf(ficresilk," %10.6f\n", -llt);
     if (stepm >= YEARM) hstepm=1;        }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      } /* end of wave */
     gradg=matrix(1,npar,1,nlstate);    } /* end of individual */
     gp=vector(1,nlstate);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     gm=vector(1,nlstate);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     for(theta=1; theta <=npar; theta++){    if(globpr==0){ /* First time we count the contributions and weights */
       for(i=1; i<=npar; i++){ /* Computes gradient */      gipmx=ipmx;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      gsw=sw;
       }    }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    return -l;
       for(i=1;i<=nlstate;i++)  }
         gp[i] = prlim[i][i];  
      
       for(i=1; i<=npar; i++) /* Computes gradient */  /*************** function likelione ***********/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  {
       for(i=1;i<=nlstate;i++)    /* This routine should help understanding what is done with 
         gm[i] = prlim[i][i];       the selection of individuals/waves and
        to check the exact contribution to the likelihood.
       for(i=1;i<=nlstate;i++)       Plotting could be done.
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];     */
     } /* End theta */    int k;
   
     trgradg =matrix(1,nlstate,1,npar);    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
     for(j=1; j<=nlstate;j++)      strcat(fileresilk,fileres);
       for(theta=1; theta <=npar; theta++)      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         trgradg[j][theta]=gradg[theta][j];        printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     for(i=1;i<=nlstate;i++)      }
       varpl[i][(int)age] =0.;      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");
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     for(i=1;i<=nlstate;i++)      for(k=1; k<=nlstate; k++) 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     fprintf(ficresvpl,"%.0f ",age );    }
     for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    *fretone=(*funcone)(p);
     fprintf(ficresvpl,"\n");    if(*globpri !=0){
     free_vector(gp,1,nlstate);      fclose(ficresilk);
     free_vector(gm,1,nlstate);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     free_matrix(gradg,1,npar,1,nlstate);      fflush(fichtm); 
     free_matrix(trgradg,1,nlstate,1,npar);    } 
   } /* End age */    return;
   }
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);  /*********** Maximum Likelihood Estimation ***************/
   
 }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
 /************ Variance of one-step probabilities  ******************/    int i,j, iter;
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    double **xi;
 {    double fret;
   int i, j=0,  i1, k1, l1, t, tj;    double fretone; /* Only one call to likelihood */
   int k2, l2, j1,  z1;    /*  char filerespow[FILENAMELENGTH];*/
   int k=0,l, cptcode;  
   int first=1, first1;  #ifdef NLOPT
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;    int creturn;
   double **dnewm,**doldm;    nlopt_opt opt;
   double *xp;    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
   double *gp, *gm;    double *lb;
   double **gradg, **trgradg;    double minf; /* the minimum objective value, upon return */
   double **mu;    double * p1; /* Shifted parameters from 0 instead of 1 */
   double age,agelim, cov[NCOVMAX];    myfunc_data dinst, *d = &dinst;
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */  #endif
   int theta;  
   char fileresprob[FILENAMELENGTH];  
   char fileresprobcov[FILENAMELENGTH];    xi=matrix(1,npar,1,npar);
   char fileresprobcor[FILENAMELENGTH];    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
   double ***varpij;        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
   strcpy(fileresprob,"prob");    strcpy(filerespow,"pow"); 
   strcat(fileresprob,fileres);    strcat(filerespow,fileres);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     printf("Problem with resultfile: %s\n", fileresprob);      printf("Problem with resultfile: %s\n", filerespow);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   }    }
   strcpy(fileresprobcov,"probcov");    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   strcat(fileresprobcov,fileres);    for (i=1;i<=nlstate;i++)
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {      for(j=1;j<=nlstate+ndeath;j++)
     printf("Problem with resultfile: %s\n", fileresprobcov);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);    fprintf(ficrespow,"\n");
   }  #ifdef POWELL
   strcpy(fileresprobcor,"probcor");    powell(p,xi,npar,ftol,&iter,&fret,func);
   strcat(fileresprobcor,fileres);  #endif
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobcor);  #ifdef NLOPT
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);  #ifdef NEWUOA
   }    opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);  #else
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);  #endif
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    lb=vector(0,npar-1);
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    nlopt_set_lower_bounds(opt, lb);
      nlopt_set_initial_step1(opt, 0.1);
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    
   fprintf(ficresprob,"# Age");    p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    d->function = func;
   fprintf(ficresprobcov,"# Age");    printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    nlopt_set_min_objective(opt, myfunc, d);
   fprintf(ficresprobcov,"# Age");    nlopt_set_xtol_rel(opt, ftol);
     if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
       printf("nlopt failed! %d\n",creturn); 
   for(i=1; i<=nlstate;i++)    }
     for(j=1; j<=(nlstate+ndeath);j++){    else {
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
       fprintf(ficresprobcov," p%1d-%1d ",i,j);      printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       fprintf(ficresprobcor," p%1d-%1d ",i,j);      iter=1; /* not equal */
     }      }
   fprintf(ficresprob,"\n");    nlopt_destroy(opt);
   fprintf(ficresprobcov,"\n");  #endif
   fprintf(ficresprobcor,"\n");    free_matrix(xi,1,npar,1,npar);
   xp=vector(1,npar);    fclose(ficrespow);
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);  
   first=1;  }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {  
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);  /**** Computes Hessian and covariance matrix ***/
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     exit(0);  {
   }    double  **a,**y,*x,pd;
   else{    double **hess;
     fprintf(ficgp,"\n# Routine varprob");    int i, j;
   }    int *indx;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {  
     printf("Problem with html file: %s\n", optionfilehtm);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     exit(0);    void lubksb(double **a, int npar, int *indx, double b[]) ;
   }    void ludcmp(double **a, int npar, int *indx, double *d) ;
   else{    double gompertz(double p[]);
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");    hess=matrix(1,npar,1,npar);
     fprintf(fichtm,"\n");  
     printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     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");    for (i=1;i<=npar;i++){
     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");      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
   }     
        hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
        
   cov[1]=1;      /*  printf(" %f ",p[i]);
   tj=cptcoveff;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}    }
   j1=0;    
   for(t=1; t<=tj;t++){    for (i=1;i<=npar;i++) {
     for(i1=1; i1<=ncodemax[t];i1++){      for (j=1;j<=npar;j++)  {
       j1++;        if (j>i) { 
                printf(".%d%d",i,j);fflush(stdout);
       if  (cptcovn>0) {          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         fprintf(ficresprob, "\n#********** Variable ");          hess[i][j]=hessij(p,delti,i,j,func,npar);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          
         fprintf(ficresprob, "**********\n#");          hess[j][i]=hess[i][j];    
         fprintf(ficresprobcov, "\n#********** Variable ");          /*printf(" %lf ",hess[i][j]);*/
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        }
         fprintf(ficresprobcov, "**********\n#");      }
            }
         fprintf(ficgp, "\n#********** Variable ");    printf("\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    fprintf(ficlog,"\n");
         fprintf(ficgp, "**********\n#");  
            printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
            fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");    
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    a=matrix(1,npar,1,npar);
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");    y=matrix(1,npar,1,npar);
            x=vector(1,npar);
         fprintf(ficresprobcor, "\n#********** Variable ");        indx=ivector(1,npar);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for (i=1;i<=npar;i++)
         fprintf(ficgp, "**********\n#");          for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       }    ludcmp(a,npar,indx,&pd);
        
       for (age=bage; age<=fage; age ++){    for (j=1;j<=npar;j++) {
         cov[2]=age;      for (i=1;i<=npar;i++) x[i]=0;
         for (k=1; k<=cptcovn;k++) {      x[j]=1;
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];      lubksb(a,npar,indx,x);
         }      for (i=1;i<=npar;i++){ 
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        matcov[i][j]=x[i];
         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]]];    }
          
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));    printf("\n#Hessian matrix#\n");
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    fprintf(ficlog,"\n#Hessian matrix#\n");
         gp=vector(1,(nlstate)*(nlstate+ndeath));    for (i=1;i<=npar;i++) { 
         gm=vector(1,(nlstate)*(nlstate+ndeath));      for (j=1;j<=npar;j++) { 
            printf("%.3e ",hess[i][j]);
         for(theta=1; theta <=npar; theta++){        fprintf(ficlog,"%.3e ",hess[i][j]);
           for(i=1; i<=npar; i++)      }
             xp[i] = x[i] + (i==theta ?delti[theta]:0);      printf("\n");
                fprintf(ficlog,"\n");
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    }
            
           k=0;    /* Recompute Inverse */
           for(i=1; i<= (nlstate); i++){    for (i=1;i<=npar;i++)
             for(j=1; j<=(nlstate+ndeath);j++){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
               k=k+1;    ludcmp(a,npar,indx,&pd);
               gp[k]=pmmij[i][j];  
             }    /*  printf("\n#Hessian matrix recomputed#\n");
           }  
              for (j=1;j<=npar;j++) {
           for(i=1; i<=npar; i++)      for (i=1;i<=npar;i++) x[i]=0;
             xp[i] = x[i] - (i==theta ?delti[theta]:0);      x[j]=1;
          lubksb(a,npar,indx,x);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      for (i=1;i<=npar;i++){ 
           k=0;        y[i][j]=x[i];
           for(i=1; i<=(nlstate); i++){        printf("%.3e ",y[i][j]);
             for(j=1; j<=(nlstate+ndeath);j++){        fprintf(ficlog,"%.3e ",y[i][j]);
               k=k+1;      }
               gm[k]=pmmij[i][j];      printf("\n");
             }      fprintf(ficlog,"\n");
           }    }
          */
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)  
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      free_matrix(a,1,npar,1,npar);
         }    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)    free_ivector(indx,1,npar);
           for(theta=1; theta <=npar; theta++)    free_matrix(hess,1,npar,1,npar);
             trgradg[j][theta]=gradg[theta][j];  
          
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);  }
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);  
          /*************** hessian matrix ****************/
         pmij(pmmij,cov,ncovmodel,x,nlstate);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
          {
         k=0;    int i;
         for(i=1; i<=(nlstate); i++){    int l=1, lmax=20;
           for(j=1; j<=(nlstate+ndeath);j++){    double k1,k2;
             k=k+1;    double p2[MAXPARM+1]; /* identical to x */
             mu[k][(int) age]=pmmij[i][j];    double res;
           }    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         }    double fx;
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)    int k=0,kmax=10;
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)    double l1;
             varpij[i][j][(int)age] = doldm[i][j];  
     fx=func(x);
         /*printf("\n%d ",(int)age);    for (i=1;i<=npar;i++) p2[i]=x[i];
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      l1=pow(10,l);
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      delts=delt;
      }*/      for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
         fprintf(ficresprob,"\n%d ",(int)age);        p2[theta]=x[theta] +delt;
         fprintf(ficresprobcov,"\n%d ",(int)age);        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
         fprintf(ficresprobcor,"\n%d ",(int)age);        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)        /*res= (k1-2.0*fx+k2)/delt/delt; */
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){        
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);  #ifdef DEBUGHESS
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         i=0;  #endif
         for (k=1; k<=(nlstate);k++){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
           for (l=1; l<=(nlstate+ndeath);l++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
             i=i++;          k=kmax;
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);        }
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
             for (j=1; j<=i;j++){          k=kmax; l=lmax*10;
               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]));        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
             }          delts=delt;
           }        }
         }/* end of loop for state */      }
       } /* end of loop for age */    }
     delti[theta]=delts;
       /* Confidence intervalle of pij  */    return res; 
       /*    
       fprintf(ficgp,"\nset noparametric;unset label");  }
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");  
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
       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);    int i;
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);    int l=1, lmax=20;
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);    double k1,k2,k3,k4,res,fx;
       */    double p2[MAXPARM+1];
     int k;
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/  
       first1=1;    fx=func(x);
       for (k2=1; k2<=(nlstate);k2++){    for (k=1; k<=2; k++) {
         for (l2=1; l2<=(nlstate+ndeath);l2++){      for (i=1;i<=npar;i++) p2[i]=x[i];
           if(l2==k2) continue;      p2[thetai]=x[thetai]+delti[thetai]/k;
           j=(k2-1)*(nlstate+ndeath)+l2;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           for (k1=1; k1<=(nlstate);k1++){      k1=func(p2)-fx;
             for (l1=1; l1<=(nlstate+ndeath);l1++){    
               if(l1==k1) continue;      p2[thetai]=x[thetai]+delti[thetai]/k;
               i=(k1-1)*(nlstate+ndeath)+l1;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
               if(i<=j) continue;      k2=func(p2)-fx;
               for (age=bage; age<=fage; age ++){    
                 if ((int)age %5==0){      p2[thetai]=x[thetai]-delti[thetai]/k;
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;      k3=func(p2)-fx;
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;    
                   mu1=mu[i][(int) age]/stepm*YEARM ;      p2[thetai]=x[thetai]-delti[thetai]/k;
                   mu2=mu[j][(int) age]/stepm*YEARM;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
                   c12=cv12/sqrt(v1*v2);      k4=func(p2)-fx;
                   /* Computing eigen value of matrix of covariance */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;  #ifdef DEBUG
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;      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);
                   /* Eigen vectors */      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);
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));  #endif
                   /*v21=sqrt(1.-v11*v11); *//* error */    }
                   v21=(lc1-v1)/cv12*v11;    return res;
                   v12=-v21;  }
                   v22=v11;  
                   tnalp=v21/v11;  /************** Inverse of matrix **************/
                   if(first1==1){  void ludcmp(double **a, int n, int *indx, double *d) 
                     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);    int i,imax,j,k; 
                   }    double big,dum,sum,temp; 
                   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);    double *vv; 
                   /*printf(fignu*/   
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    vv=vector(1,n); 
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */    *d=1.0; 
                   if(first==1){    for (i=1;i<=n;i++) { 
                     first=0;      big=0.0; 
                     fprintf(ficgp,"\nset parametric;unset label");      for (j=1;j<=n;j++) 
                     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);        if ((temp=fabs(a[i][j])) > big) big=temp; 
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
                     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>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);      vv[i]=1.0/big; 
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);    } 
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);    for (j=1;j<=n;j++) { 
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);      for (i=1;i<j;i++) { 
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);        sum=a[i][j]; 
                     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 (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\        a[i][j]=sum; 
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));      } 
                   }else{      big=0.0; 
                     first=0;      for (i=j;i<=n;i++) { 
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);        sum=a[i][j]; 
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);        for (k=1;k<j;k++) 
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\          sum -= a[i][k]*a[k][j]; 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\        a[i][j]=sum; 
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));        if ( (dum=vv[i]*fabs(sum)) >= big) { 
                   }/* if first */          big=dum; 
                 } /* age mod 5 */          imax=i; 
               } /* end loop age */        } 
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);      } 
               first=1;      if (j != imax) { 
             } /*l12 */        for (k=1;k<=n;k++) { 
           } /* k12 */          dum=a[imax][k]; 
         } /*l1 */          a[imax][k]=a[j][k]; 
       }/* k1 */          a[j][k]=dum; 
     } /* loop covariates */        } 
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);        *d = -(*d); 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        vv[imax]=vv[j]; 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      } 
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);      indx[j]=imax; 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      if (a[j][j] == 0.0) a[j][j]=TINY; 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      if (j != n) { 
   }        dum=1.0/(a[j][j]); 
   free_vector(xp,1,npar);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   fclose(ficresprob);      } 
   fclose(ficresprobcov);    } 
   fclose(ficresprobcor);    free_vector(vv,1,n);  /* Doesn't work */
   fclose(ficgp);  ;
   fclose(fichtm);  } 
 }  
   void lubksb(double **a, int n, int *indx, double b[]) 
   { 
 /******************* Printing html file ***********/    int i,ii=0,ip,j; 
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    double sum; 
                   int lastpass, int stepm, int weightopt, char model[],\   
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    for (i=1;i<=n;i++) { 
                   int popforecast, int estepm ,\      ip=indx[i]; 
                   double jprev1, double mprev1,double anprev1, \      sum=b[ip]; 
                   double jprev2, double mprev2,double anprev2){      b[ip]=b[i]; 
   int jj1, k1, i1, cpt;      if (ii) 
   /*char optionfilehtm[FILENAMELENGTH];*/        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {      else if (sum) ii=i; 
     printf("Problem with %s \n",optionfilehtm), exit(0);      b[i]=sum; 
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);    } 
   }    for (i=n;i>=1;i--) { 
       sum=b[i]; 
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
  - 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      b[i]=sum/a[i][i]; 
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    } 
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n  } 
  - Life expectancies by age and initial health status (estepm=%2d months):  
    <a href=\"e%s\">e%s</a> <br>\n</li>", \  void pstamp(FILE *fichier)
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);  {
     fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  }
   
  m=cptcoveff;  /************ Frequencies ********************/
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
   {  /* Some frequencies */
  jj1=0;    
  for(k1=1; k1<=m;k1++){    int i, m, jk, j1, bool, z1,j;
    for(i1=1; i1<=ncodemax[k1];i1++){    int first;
      jj1++;    double ***freq; /* Frequencies */
      if (cptcovn > 0) {    double *pp, **prop;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    double pos,posprop, k2, dateintsum=0,k2cpt=0;
        for (cpt=1; cpt<=cptcoveff;cpt++)    char fileresp[FILENAMELENGTH];
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    pp=vector(1,nlstate);
      }    prop=matrix(1,nlstate,iagemin,iagemax+3);
      /* Pij */    strcpy(fileresp,"p");
      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>    strcat(fileresp,fileres);
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        if((ficresp=fopen(fileresp,"w"))==NULL) {
      /* Quasi-incidences */      printf("Problem with prevalence resultfile: %s\n", fileresp);
      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>      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      exit(0);
        /* Stable prevalence in each health state */    }
        for(cpt=1; cpt<nlstate;cpt++){    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    j1=0;
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
        }    j=cptcoveff;
      for(cpt=1; cpt<=nlstate;cpt++) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>  
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    first=1;
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
 health expectancies in states (1) and (2): e%s%d.png<br>    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    /*    j1++;
    } /* end i1 */  */
  }/* End k1 */    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
  fprintf(fichtm,"</ul>");        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n          for (jk=-5; jk<=nlstate+ndeath; jk++)  
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n            for(m=iagemin; m <= iagemax+3; m++)
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n              freq[i][jk][m]=0;
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n        
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n        for (i=1; i<=nlstate; i++)  
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n          for(m=iagemin; m <= iagemax+3; m++)
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n            prop[i][m]=0;
  - 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);        
         dateintsum=0;
  if(popforecast==1) fprintf(fichtm,"\n        k2cpt=0;
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n        for (i=1; i<=imx; i++) {
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n          bool=1;
         <br>",fileres,fileres,fileres,fileres);          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
  else            for (z1=1; z1<=cptcoveff; z1++)       
    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);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
                 bool=0;
  m=cptcoveff;                /* 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", 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                  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);*/
  jj1=0;                /* 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<=m;k1++){              } 
    for(i1=1; i1<=ncodemax[k1];i1++){          }
      jj1++;   
      if (cptcovn > 0) {          if (bool==1){
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            for(m=firstpass; m<=lastpass; m++){
        for (cpt=1; cpt<=cptcoveff;cpt++)              k2=anint[m][i]+(mint[m][i]/12.);
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
      }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
      for(cpt=1; cpt<=nlstate;cpt++) {                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident                if (m<lastpass) {
 interval) in state (%d): v%s%d%d.png <br>                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                    freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
      }                }
    } /* end i1 */                
  }/* End k1 */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
  fprintf(fichtm,"</ul>");                  dateintsum=dateintsum+k2;
 fclose(fichtm);                  k2cpt++;
 }                }
                 /*}*/
 /******************* Gnuplot file **************/            }
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){          }
         } /* end i */
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;         
   int ng;        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        pstamp(ficresp);
     printf("Problem with file %s",optionfilegnuplot);        if  (cptcovn>0) {
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);          fprintf(ficresp, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
 #ifdef windows          fprintf(ficlog, "\n#********** Variable "); 
     fprintf(ficgp,"cd \"%s\" \n",pathc);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 #endif          fprintf(ficlog, "**********\n#");
 m=pow(2,cptcoveff);        }
          for(i=1; i<=nlstate;i++) 
  /* 1eme*/          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   for (cpt=1; cpt<= nlstate ; cpt ++) {        fprintf(ficresp, "\n");
    for (k1=1; k1<= m ; k1 ++) {        
         for(i=iagemin; i <= iagemax+3; i++){
 #ifdef windows          if(i==iagemax+3){
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);            fprintf(ficlog,"Total");
      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);          }else{
 #endif            if(first==1){
 #ifdef unix              first=0;
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);              printf("See log file for details...\n");
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);            }
 #endif            fprintf(ficlog,"Age %d", i);
           }
 for (i=1; i<= nlstate ; i ++) {          for(jk=1; jk <=nlstate ; jk++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              pp[jk] += freq[jk][m][i]; 
 }          }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          for(jk=1; jk <=nlstate ; jk++){
     for (i=1; i<= nlstate ; i ++) {            for(m=-1, pos=0; m <=0 ; m++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              pos += freq[jk][m][i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");            if(pp[jk]>=1.e-10){
 }              if(first==1){
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      for (i=1; i<= nlstate ; i ++) {              }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   else fprintf(ficgp," \%%*lf (\%%*lf)");            }else{
 }                if(first==1)
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 #ifdef unix              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");            }
 #endif          }
    }  
   }          for(jk=1; jk <=nlstate ; jk++){
   /*2 eme*/            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
   for (k1=1; k1<= m ; k1 ++) {          }       
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);            pos += pp[jk];
                posprop += prop[jk][i];
     for (i=1; i<= nlstate+1 ; i ++) {          }
       k=2*i;          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);            if(pos>=1.e-5){
       for (j=1; j<= nlstate+1 ; j ++) {              if(first==1)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   else fprintf(ficgp," \%%*lf (\%%*lf)");              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 }              }else{
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");              if(first==1)
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for (j=1; j<= nlstate+1 ; j ++) {            }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            if( i <= iagemax){
         else fprintf(ficgp," \%%*lf (\%%*lf)");              if(pos>=1.e-5){
 }                  fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       fprintf(ficgp,"\" t\"\" w l 0,");                /*probs[i][jk][j1]= pp[jk]/pos;*/
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
       for (j=1; j<= nlstate+1 ; j ++) {              }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              else
   else fprintf(ficgp," \%%*lf (\%%*lf)");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
 }              }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          }
       else fprintf(ficgp,"\" t\"\" w l 0,");          
     }          for(jk=-1; jk <=nlstate+ndeath; jk++)
   }            for(m=-1; m <=nlstate+ndeath; m++)
                if(freq[jk][m][i] !=0 ) {
   /*3eme*/              if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   for (k1=1; k1<= m ; k1 ++) {                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     for (cpt=1; cpt<= nlstate ; cpt ++) {              }
       k=2+nlstate*(2*cpt-2);          if(i <= iagemax)
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);            fprintf(ficresp,"\n");
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);          if(first==1)
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);            printf("Others in log...\n");
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          fprintf(ficlog,"\n");
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        }
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%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);    dateintmean=dateintsum/k2cpt; 
    
 */    fclose(ficresp);
       for (i=1; i< nlstate ; i ++) {    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
         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);    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       }    /* End of Freq */
     }  }
   }  
    /************ Prevalence ********************/
   /* CV preval stat */  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 (k1=1; k1<= m ; k1 ++) {  {  
     for (cpt=1; cpt<nlstate ; cpt ++) {    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       k=3;       in each health status at the date of interview (if between dateprev1 and dateprev2).
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);       We still use firstpass and lastpass as another selection.
       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);    */
    
       for (i=1; i< nlstate ; i ++)    int i, m, jk, j1, bool, z1,j;
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    double **prop;
          double posprop; 
       l=3+(nlstate+ndeath)*cpt;    double  y2; /* in fractional years */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    int iagemin, iagemax;
       for (i=1; i< nlstate ; i ++) {    int first; /** to stop verbosity which is redirected to log file */
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);    iagemin= (int) agemin;
       }    iagemax= (int) agemax;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      /*pp=vector(1,nlstate);*/
     }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   }      /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
      j1=0;
   /* proba elementaires */    
    for(i=1,jk=1; i <=nlstate; i++){    /*j=cptcoveff;*/
     for(k=1; k <=(nlstate+ndeath); k++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       if (k != i) {    
         for(j=1; j <=ncovmodel; j++){    first=1;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
           jk++;      /*for(i1=1; i1<=ncodemax[k1];i1++){
           fprintf(ficgp,"\n");        j1++;*/
         }        
       }        for (i=1; i<=nlstate; i++)  
     }          for(m=iagemin; m <= iagemax+3; m++)
    }            prop[i][m]=0.0;
        
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/        for (i=1; i<=imx; i++) { /* Each individual */
      for(jk=1; jk <=m; jk++) {          bool=1;
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);          if  (cptcovn>0) {
        if (ng==2)            for (z1=1; z1<=cptcoveff; z1++) 
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
        else                bool=0;
          fprintf(ficgp,"\nset title \"Probability\"\n");          } 
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          if (bool==1) { 
        i=1;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
        for(k2=1; k2<=nlstate; k2++) {              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
          k3=i;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
          for(k=1; k<=(nlstate+ndeath); k++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
            if (k != k2){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
              if(ng==2)                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
              else                  /*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]]);*/
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
              ij=1;                  prop[s[m][i]][iagemax+3] += weight[i]; 
              for(j=3; j <=ncovmodel; j++) {                } 
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              }
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            } /* end selection of waves */
                  ij++;          }
                }        }
                else        for(i=iagemin; i <= iagemax+3; i++){  
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
              }            posprop += prop[jk][i]; 
              fprintf(ficgp,")/(1");          } 
                        
              for(k1=1; k1 <=nlstate; k1++){            for(jk=1; jk <=nlstate ; jk++){     
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            if( i <=  iagemax){ 
                ij=1;              if(posprop>=1.e-5){ 
                for(j=3; j <=ncovmodel; j++){                probs[i][jk][j1]= prop[jk][i]/posprop;
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              } else{
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                if(first==1){
                    ij++;                  first=0;
                  }                  printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
                  else                }
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              }
                }            } 
                fprintf(ficgp,")");          }/* end jk */ 
              }        }/* end i */ 
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);      /*} *//* end i1 */
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    } /* end j1 */
              i=i+ncovmodel;    
            }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
          } /* end k */    /*free_vector(pp,1,nlstate);*/
        } /* end k2 */    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
      } /* end jk */  }  /* End of prevalence */
    } /* end ng */  
    fclose(ficgp);  /************* Waves Concatenation ***************/
 }  /* end gnuplot */  
   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)
   {
 /*************** Moving average **************/    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){       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
   int i, cpt, cptcod;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)       and mw[mi+1][i]. dh depends on stepm.
       for (i=1; i<=nlstate;i++)       */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)  
           mobaverage[(int)agedeb][i][cptcod]=0.;    int i, mi, m;
        /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){       double sum=0., jmean=0.;*/
       for (i=1; i<=nlstate;i++){    int first;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    int j, k=0,jk, ju, jl;
           for (cpt=0;cpt<=4;cpt++){    double sum=0.;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    first=0;
           }    jmin=100000;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    jmax=-1;
         }    jmean=0.;
       }    for(i=1; i<=imx; i++){
     }      mi=0;
          m=firstpass;
 }      while(s[m][i] <= nlstate){
         if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           mw[++mi][i]=m;
 /************** Forecasting ******************/        if(m >=lastpass)
 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){          break;
          else
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          m++;
   int *popage;      }/* end while */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      if (s[m][i] > nlstate){
   double *popeffectif,*popcount;        mi++;     /* Death is another wave */
   double ***p3mat;        /* if(mi==0)  never been interviewed correctly before death */
   char fileresf[FILENAMELENGTH];           /* Only death is a correct wave */
         mw[mi][i]=m;
  agelim=AGESUP;      }
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
       wav[i]=mi;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      if(mi==0){
          nbwarn++;
          if(first==0){
   strcpy(fileresf,"f");          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   strcat(fileresf,fileres);          first=1;
   if((ficresf=fopen(fileresf,"w"))==NULL) {        }
     printf("Problem with forecast resultfile: %s\n", fileresf);        if(first==1){
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
   }        }
   printf("Computing forecasting: result on file '%s' \n", fileresf);      } /* end mi==0 */
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    } /* End individuals */
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
   if (mobilav==1) {        if (stepm <=0)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          dh[mi][i]=1;
     movingaverage(agedeb, fage, ageminpar, mobaverage);        else{
   }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             if (agedc[i] < 2*AGESUP) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   if (stepm<=12) stepsize=1;              if(j==0) j=1;  /* Survives at least one month after exam */
                else if(j<0){
   agelim=AGESUP;                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]);
   hstepm=1;                j=1; /* Temporary Dangerous patch */
   hstepm=hstepm/stepm;                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);
   yp1=modf(dateintmean,&yp);                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]);
   anprojmean=yp;                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);
   yp2=modf((yp1*12),&yp);              }
   mprojmean=yp;              k=k+1;
   yp1=modf((yp2*30.5),&yp);              if (j >= jmax){
   jprojmean=yp;                jmax=j;
   if(jprojmean==0) jprojmean=1;                ijmax=i;
   if(mprojmean==0) jprojmean=1;              }
                if (j <= jmin){
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);                jmin=j;
                  ijmin=i;
   for(cptcov=1;cptcov<=i2;cptcov++){              }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              sum=sum+j;
       k=k+1;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       fprintf(ficresf,"\n#******");              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       for(j=1;j<=cptcoveff;j++) {            }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          }
       }          else{
       fprintf(ficresf,"******\n");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       fprintf(ficresf,"# StartingAge FinalAge");  /*        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]); */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  
                  k=k+1;
                  if (j >= jmax) {
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {              jmax=j;
         fprintf(ficresf,"\n");              ijmax=i;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);              }
             else if (j <= jmin){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              jmin=j;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              ijmin=i;
           nhstepm = nhstepm/hstepm;            }
                      /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            /*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]);*/
           oldm=oldms;savm=savms;            if(j<0){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                nberr++;
                      printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           for (h=0; h<=nhstepm; h++){              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]);
             if (h==(int) (calagedate+YEARM*cpt)) {            }
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);            sum=sum+j;
             }          }
             for(j=1; j<=nlstate+ndeath;j++) {          jk= j/stepm;
               kk1=0.;kk2=0;          jl= j -jk*stepm;
               for(i=1; i<=nlstate;i++) {                        ju= j -(jk+1)*stepm;
                 if (mobilav==1)          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            if(jl==0){
                 else {              dh[mi][i]=jk;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              bh[mi][i]=0;
                 }            }else{ /* We want a negative bias in order to only have interpolation ie
                                    * to avoid the price of an extra matrix product in likelihood */
               }              dh[mi][i]=jk+1;
               if (h==(int)(calagedate+12*cpt)){              bh[mi][i]=ju;
                 fprintf(ficresf," %.3f", kk1);            }
                                  }else{
               }            if(jl <= -ju){
             }              dh[mi][i]=jk;
           }              bh[mi][i]=jl;       /* bias is positive if real duration
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                                   * is higher than the multiple of stepm and negative otherwise.
         }                                   */
       }            }
     }            else{
   }              dh[mi][i]=jk+1;
                      bh[mi][i]=ju;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
             if(dh[mi][i]==0){
   fclose(ficresf);              dh[mi][i]=1; /* At least one step */
 }              bh[mi][i]=ju; /* At least one step */
 /************** Forecasting ******************/              /*  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);*/
 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){            }
            } /* end if mle */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        }
   int *popage;      } /* end wave */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    }
   double *popeffectif,*popcount;    jmean=sum/k;
   double ***p3mat,***tabpop,***tabpopprev;    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);
   char filerespop[FILENAMELENGTH];    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);
    }
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*********** Tricode ****************************/
   agelim=AGESUP;  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  {
      /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
      /* Boring subroutine which should only output nbcode[Tvar[j]][k]
       * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
   strcpy(filerespop,"pop");    /* nbcode[Tvar[j]][1]= 
   strcat(filerespop,fileres);    */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", filerespop);    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);    int modmaxcovj=0; /* Modality max of covariates j */
   }    int cptcode=0; /* Modality max of covariates j */
   printf("Computing forecasting: result on file '%s' \n", filerespop);    int modmincovj=0; /* Modality min of covariates j */
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);  
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    cptcoveff=0; 
    
   if (mobilav==1) {    for (k=-1; k < maxncov; k++) Ndum[k]=0;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }    /* Loop on covariates without age and products */
     for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
   stepsize=(int) (stepm+YEARM-1)/YEARM;      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
   if (stepm<=12) stepsize=1;                                 modality of this covariate Vj*/ 
          ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
   agelim=AGESUP;                                      * If product of Vn*Vm, still boolean *:
                                        * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
   hstepm=1;                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
   hstepm=hstepm/stepm;        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                          modality of the nth covariate of individual i. */
   if (popforecast==1) {        if (ij > modmaxcovj)
     if((ficpop=fopen(popfile,"r"))==NULL) {          modmaxcovj=ij; 
       printf("Problem with population file : %s\n",popfile);exit(0);        else if (ij < modmincovj) 
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);          modmincovj=ij; 
     }        if ((ij < -1) && (ij > NCOVMAX)){
     popage=ivector(0,AGESUP);          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
     popeffectif=vector(0,AGESUP);          exit(1);
     popcount=vector(0,AGESUP);        }else
            Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
     i=1;          /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
            /* getting the maximum value of the modality of the covariate
     imx=i;           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];           female is 1, then modmaxcovj=1.*/
   }      }
       printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   for(cptcov=1;cptcov<=i2;cptcov++){      cptcode=modmaxcovj;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
       k=k+1;     /*for (i=0; i<=cptcode; i++) {*/
       fprintf(ficrespop,"\n#******");      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
       for(j=1;j<=cptcoveff;j++) {        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
       }          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
       fprintf(ficrespop,"******\n");        }
       fprintf(ficrespop,"# Age");        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
       if (popforecast==1)  fprintf(ficrespop," [Population]");      } /* Ndum[-1] number of undefined modalities */
        
       for (cpt=0; cpt<=0;cpt++) {      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        /* 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;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){         modmincovj=3; modmaxcovj = 7;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
           nhstepm = nhstepm/hstepm;         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
                   variables V1_1 and V1_2.
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         nbcode[Tvar[j]][ij]=k;
           oldm=oldms;savm=savms;         nbcode[Tvar[j]][1]=0;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);           nbcode[Tvar[j]][2]=1;
                 nbcode[Tvar[j]][3]=2;
           for (h=0; h<=nhstepm; h++){      */
             if (h==(int) (calagedate+YEARM*cpt)) {      ij=1; /* ij is similar to i but can jumps over null modalities */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
             }        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
             for(j=1; j<=nlstate+ndeath;j++) {          /*recode from 0 */
               kk1=0.;kk2=0;          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
               for(i=1; i<=nlstate;i++) {                          nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
                 if (mobilav==1)                                       k is a modality. If we have model=V1+V1*sex 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
                 else {            ij++;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          }
                 }          if (ij > ncodemax[j]) break; 
               }        }  /* end of loop on */
               if (h==(int)(calagedate+12*cpt)){      } /* end of loop on modality */ 
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
                   /*fprintf(ficrespop," %.3f", kk1);    
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
               }    
             }    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
             for(i=1; i<=nlstate;i++){     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
               kk1=0.;     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
                 for(j=1; j<=nlstate;j++){     Ndum[ij]++; 
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];   } 
                 }  
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];   ij=1;
             }   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)     if((Ndum[i]!=0) && (i<=ncovcol)){
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
           }       Tvaraff[ij]=i; /*For printing (unclear) */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       ij++;
         }     }else
       }         Tvaraff[ij]=0;
     }
   /******/   ij--;
    cptcoveff=ij; /*Number of total covariates*/
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;  /*********** Health Expectancies ****************/
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    {
           for (h=0; h<=nhstepm; h++){    /* Health expectancies, no variances */
             if (h==(int) (calagedate+YEARM*cpt)) {    int i, j, nhstepm, hstepm, h, nstepm;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    int nhstepma, nstepma; /* Decreasing with age */
             }    double age, agelim, hf;
             for(j=1; j<=nlstate+ndeath;j++) {    double ***p3mat;
               kk1=0.;kk2=0;    double eip;
               for(i=1; i<=nlstate;i++) {                
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        pstamp(ficreseij);
               }    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    fprintf(ficreseij,"# Age");
             }    for(i=1; i<=nlstate;i++){
           }      for(j=1; j<=nlstate;j++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficreseij," e%1d%1d ",i,j);
         }      }
       }      fprintf(ficreseij," e%1d. ",i);
    }    }
   }    fprintf(ficreseij,"\n");
    
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    
     if(estepm < stepm){
   if (popforecast==1) {      printf ("Problem %d lower than %d\n",estepm, stepm);
     free_ivector(popage,0,AGESUP);    }
     free_vector(popeffectif,0,AGESUP);    else  hstepm=estepm;   
     free_vector(popcount,0,AGESUP);    /* We compute the life expectancy from trapezoids spaced every estepm months
   }     * This is mainly to measure the difference between two models: for example
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * if stepm=24 months pijx are given only every 2 years and by summing them
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   fclose(ficrespop);     * progression in between and thus overestimating or underestimating according
 }     * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
 /***********************************************/     * to compare the new estimate of Life expectancy with the same linear 
 /**************** Main Program *****************/     * hypothesis. A more precise result, taking into account a more precise
 /***********************************************/     * curvature will be obtained if estepm is as small as stepm. */
   
 int main(int argc, char *argv[])    /* For example we decided to compute the life expectancy with the smallest unit */
 {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;       nstepm is the number of stepm from age to agelin. 
   double agedeb, agefin,hf;       Look at hpijx to understand the reason of that which relies in memory size
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   double fret;       survival function given by stepm (the optimization length). Unfortunately it
   double **xi,tmp,delta;       means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double dum; /* Dummy variable */       results. So we changed our mind and took the option of the best precision.
   double ***p3mat;    */
   int *indx;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   char line[MAXLINE], linepar[MAXLINE];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];    agelim=AGESUP;
   int firstobs=1, lastobs=10;    /* If stepm=6 months */
   int sdeb, sfin; /* Status at beginning and end */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   int c,  h , cpt,l;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   int ju,jl, mi;      
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  /* nhstepm age range expressed in number of stepm */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   int mobilav=0,popforecast=0;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   int hstepm, nhstepm;    /* if (stepm >= YEARM) hstepm=1;*/
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double bage, fage, age, agelim, agebase;  
   double ftolpl=FTOL;    for (age=bage; age<=fage; age ++){ 
   double **prlim;      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   double *severity;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   double ***param; /* Matrix of parameters */      /* if (stepm >= YEARM) hstepm=1;*/
   double  *p;      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */      /* If stepm=6 months */
   double *delti; /* Scale */      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   double ***eij, ***vareij;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   double **varpl; /* Variances of prevalence limits by age */      
   double *epj, vepp;      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   double kk1, kk2;      
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        
       printf("%d|",(int)age);fflush(stdout);
   char *alph[]={"a","a","b","c","d","e"}, str[4];      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       
       /* Computing expectancies */
   char z[1]="c", occ;      for(i=1; i<=nlstate;i++)
 #include <sys/time.h>        for(j=1; j<=nlstate;j++)
 #include <time.h>          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
              
   /* long total_usecs;            /* 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]);*/
   struct timeval start_time, end_time;  
            }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  
   getcwd(pathcd, size);      fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
   printf("\n%s",version);        eip=0;
   if(argc <=1){        for(j=1; j<=nlstate;j++){
     printf("\nEnter the parameter file name: ");          eip +=eij[i][j][(int)age];
     scanf("%s",pathtot);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   }        }
   else{        fprintf(ficreseij,"%9.4f", eip );
     strcpy(pathtot,argv[1]);      }
   }      fprintf(ficreseij,"\n");
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      
   /*cygwin_split_path(pathtot,path,optionfile);    }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /* cutv(path,optionfile,pathtot,'\\');*/    printf("\n");
     fprintf(ficlog,"\n");
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  }
   chdir(path);  
   replace(pathc,path);  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[] )
   
 /*-------- arguments in the command line --------*/  {
     /* Covariances of health expectancies eij and of total life expectancies according
   /* Log file */     to initial status i, ei. .
   strcat(filelog, optionfilefiname);    */
   strcat(filelog,".log");    /* */    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   if((ficlog=fopen(filelog,"w"))==NULL)    {    int nhstepma, nstepma; /* Decreasing with age */
     printf("Problem with logfile %s\n",filelog);    double age, agelim, hf;
     goto end;    double ***p3matp, ***p3matm, ***varhe;
   }    double **dnewm,**doldm;
   fprintf(ficlog,"Log filename:%s\n",filelog);    double *xp, *xm;
   fprintf(ficlog,"\n%s",version);    double **gp, **gm;
   fprintf(ficlog,"\nEnter the parameter file name: ");    double ***gradg, ***trgradg;
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    int theta;
   fflush(ficlog);  
     double eip, vip;
   /* */  
   strcpy(fileres,"r");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   strcat(fileres, optionfilefiname);    xp=vector(1,npar);
   strcat(fileres,".txt");    /* Other files have txt extension */    xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
   /*---------arguments file --------*/    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    pstamp(ficresstdeij);
     printf("Problem with optionfile %s\n",optionfile);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);    fprintf(ficresstdeij,"# Age");
     goto end;    for(i=1; i<=nlstate;i++){
   }      for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   strcpy(filereso,"o");      fprintf(ficresstdeij," e%1d. ",i);
   strcat(filereso,fileres);    }
   if((ficparo=fopen(filereso,"w"))==NULL) {    fprintf(ficresstdeij,"\n");
     printf("Problem with Output resultfile: %s\n", filereso);  
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);    pstamp(ficrescveij);
     goto end;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   }    fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */      for(j=1; j<=nlstate;j++){
   while((c=getc(ficpar))=='#' && c!= EOF){        cptj= (j-1)*nlstate+i;
     ungetc(c,ficpar);        for(i2=1; i2<=nlstate;i2++)
     fgets(line, MAXLINE, ficpar);          for(j2=1; j2<=nlstate;j2++){
     puts(line);            cptj2= (j2-1)*nlstate+i2;
     fputs(line,ficparo);            if(cptj2 <= cptj)
   }              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
   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);    fprintf(ficrescveij,"\n");
   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);    if(estepm < stepm){
 while((c=getc(ficpar))=='#' && c!= EOF){      printf ("Problem %d lower than %d\n",estepm, stepm);
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    else  hstepm=estepm;   
     puts(line);    /* We compute the life expectancy from trapezoids spaced every estepm months
     fputs(line,ficparo);     * 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
   ungetc(c,ficpar);     * we are calculating an estimate of the Life Expectancy assuming a linear 
       * progression in between and thus overestimating or underestimating according
         * to the curvature of the survival function. If, for the same date, we 
   covar=matrix(0,NCOVMAX,1,n);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   cptcovn=0;     * to compare the new estimate of Life expectancy with the same linear 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    /* 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. 
   /* Read guess parameters */       nhstepm is the number of hstepm from age to agelim 
   /* Reads comments: lines beginning with '#' */       nstepm is the number of stepm from age to agelin. 
   while((c=getc(ficpar))=='#' && c!= EOF){       Look at hpijx to understand the reason of that which relies in memory size
     ungetc(c,ficpar);       and note for a fixed period like estepm months */
     fgets(line, MAXLINE, ficpar);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     puts(line);       survival function given by stepm (the optimization length). Unfortunately it
     fputs(line,ficparo);       means that if the survival funtion is printed only each two years of age and if
   }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   ungetc(c,ficpar);       results. So we changed our mind and took the option of the best precision.
      */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     for(i=1; i <=nlstate; i++)  
     for(j=1; j <=nlstate+ndeath-1; j++){    /* If stepm=6 months */
       fscanf(ficpar,"%1d%1d",&i1,&j1);    /* nhstepm age range expressed in number of stepm */
       fprintf(ficparo,"%1d%1d",i1,j1);    agelim=AGESUP;
       if(mle==1)    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
         printf("%1d%1d",i,j);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       fprintf(ficlog,"%1d%1d",i,j);    /* if (stepm >= YEARM) hstepm=1;*/
       for(k=1; k<=ncovmodel;k++){    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         fscanf(ficpar," %lf",&param[i][j][k]);    
         if(mle==1){    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           printf(" %lf",param[i][j][k]);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficlog," %lf",param[i][j][k]);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         }    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
         else    gp=matrix(0,nhstepm,1,nlstate*nlstate);
           fprintf(ficlog," %lf",param[i][j][k]);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
         fprintf(ficparo," %lf",param[i][j][k]);  
       }    for (age=bage; age<=fage; age ++){ 
       fscanf(ficpar,"\n");      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       if(mle==1)      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         printf("\n");      /* if (stepm >= YEARM) hstepm=1;*/
       fprintf(ficlog,"\n");      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       fprintf(ficparo,"\n");  
     }      /* If stepm=6 months */
        /* Computed by stepm unit matrices, product of hstepma matrices, stored
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
   p=param[1][1];      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    
   /* Reads comments: lines beginning with '#' */      /* Computing  Variances of health expectancies */
   while((c=getc(ficpar))=='#' && c!= EOF){      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     ungetc(c,ficpar);         decrease memory allocation */
     fgets(line, MAXLINE, ficpar);      for(theta=1; theta <=npar; theta++){
     puts(line);        for(i=1; i<=npar; i++){ 
     fputs(line,ficparo);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }          xm[i] = x[i] - (i==theta ?delti[theta]:0);
   ungetc(c,ficpar);        }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    
   for(i=1; i <=nlstate; i++){        for(j=1; j<= nlstate; j++){
     for(j=1; j <=nlstate+ndeath-1; j++){          for(i=1; i<=nlstate; i++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);            for(h=0; h<=nhstepm-1; h++){
       printf("%1d%1d",i,j);              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
       fprintf(ficparo,"%1d%1d",i1,j1);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
       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]);       
       }        for(ij=1; ij<= nlstate*nlstate; ij++)
       fscanf(ficpar,"\n");          for(h=0; h<=nhstepm-1; h++){
       printf("\n");            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
       fprintf(ficparo,"\n");          }
     }      }/* End theta */
   }      
   delti=delti3[1][1];      
        for(h=0; h<=nhstepm-1; h++)
   /* Reads comments: lines beginning with '#' */        for(j=1; j<=nlstate*nlstate;j++)
   while((c=getc(ficpar))=='#' && c!= EOF){          for(theta=1; theta <=npar; theta++)
     ungetc(c,ficpar);            trgradg[h][j][theta]=gradg[h][theta][j];
     fgets(line, MAXLINE, ficpar);      
     puts(line);  
     fputs(line,ficparo);       for(ij=1;ij<=nlstate*nlstate;ij++)
   }        for(ji=1;ji<=nlstate*nlstate;ji++)
   ungetc(c,ficpar);          varhe[ij][ji][(int)age] =0.;
    
   matcov=matrix(1,npar,1,npar);       printf("%d|",(int)age);fflush(stdout);
   for(i=1; i <=npar; i++){       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     fscanf(ficpar,"%s",&str);       for(h=0;h<=nhstepm-1;h++){
     if(mle==1)        for(k=0;k<=nhstepm-1;k++){
       printf("%s",str);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     fprintf(ficlog,"%s",str);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     fprintf(ficparo,"%s",str);          for(ij=1;ij<=nlstate*nlstate;ij++)
     for(j=1; j <=i; j++){            for(ji=1;ji<=nlstate*nlstate;ji++)
       fscanf(ficpar," %le",&matcov[i][j]);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       if(mle==1){        }
         printf(" %.5le",matcov[i][j]);      }
         fprintf(ficlog," %.5le",matcov[i][j]);  
       }      /* Computing expectancies */
       else      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
         fprintf(ficlog," %.5le",matcov[i][j]);      for(i=1; i<=nlstate;i++)
       fprintf(ficparo," %.5le",matcov[i][j]);        for(j=1; j<=nlstate;j++)
     }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     fscanf(ficpar,"\n");            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
     if(mle==1)            
       printf("\n");            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     fprintf(ficlog,"\n");  
     fprintf(ficparo,"\n");          }
   }  
   for(i=1; i <=npar; i++)      fprintf(ficresstdeij,"%3.0f",age );
     for(j=i+1;j<=npar;j++)      for(i=1; i<=nlstate;i++){
       matcov[i][j]=matcov[j][i];        eip=0.;
            vip=0.;
   if(mle==1)        for(j=1; j<=nlstate;j++){
     printf("\n");          eip += eij[i][j][(int)age];
   fprintf(ficlog,"\n");          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
     /*-------- Rewriting paramater file ----------*/        }
      strcpy(rfileres,"r");    /* "Rparameterfile */        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/      }
      strcat(rfileres,".");    /* */      fprintf(ficresstdeij,"\n");
      strcat(rfileres,optionfilext);    /* Other files have txt extension */  
     if((ficres =fopen(rfileres,"w"))==NULL) {      fprintf(ficrescveij,"%3.0f",age );
       printf("Problem writing new parameter file: %s\n", fileres);goto end;      for(i=1; i<=nlstate;i++)
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;        for(j=1; j<=nlstate;j++){
     }          cptj= (j-1)*nlstate+i;
     fprintf(ficres,"#%s\n",version);          for(i2=1; i2<=nlstate;i2++)
                for(j2=1; j2<=nlstate;j2++){
     /*-------- data file ----------*/              cptj2= (j2-1)*nlstate+i2;
     if((fic=fopen(datafile,"r"))==NULL)    {              if(cptj2 <= cptj)
       printf("Problem with datafile: %s\n", datafile);goto end;                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;            }
     }        }
       fprintf(ficrescveij,"\n");
     n= lastobs;     
     severity = vector(1,maxwav);    }
     outcome=imatrix(1,maxwav+1,1,n);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     num=ivector(1,n);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     moisnais=vector(1,n);    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     annais=vector(1,n);    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     moisdc=vector(1,n);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     andc=vector(1,n);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     agedc=vector(1,n);    printf("\n");
     cod=ivector(1,n);    fprintf(ficlog,"\n");
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    free_vector(xm,1,npar);
     mint=matrix(1,maxwav,1,n);    free_vector(xp,1,npar);
     anint=matrix(1,maxwav,1,n);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     s=imatrix(1,maxwav+1,1,n);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     adl=imatrix(1,maxwav+1,1,n);        free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     tab=ivector(1,NCOVMAX);  }
     ncodemax=ivector(1,8);  
   /************ Variance ******************/
     i=1;  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
     while (fgets(line, MAXLINE, fic) != NULL)    {  {
       if ((i >= firstobs) && (i <=lastobs)) {    /* Variance of health expectancies */
            /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
         for (j=maxwav;j>=1;j--){    /* double **newm;*/
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    double **dnewm,**doldm;
           strcpy(line,stra);    double **dnewmp,**doldmp;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    int i, j, nhstepm, hstepm, h, nstepm ;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    int k;
         }    double *xp;
            double **gp, **gm;  /* for var eij */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    double ***gradg, ***trgradg; /*for var eij */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    double ***p3mat;
     double age,agelim, hf;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    double ***mobaverage;
         for (j=ncovcol;j>=1;j--){    int theta;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    char digit[4];
         }    char digitp[25];
         num[i]=atol(stra);  
            char fileresprobmorprev[FILENAMELENGTH];
         /*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;}*/    if(popbased==1){
       if(mobilav!=0)
         i=i+1;        strcpy(digitp,"-populbased-mobilav-");
       }      else strcpy(digitp,"-populbased-nomobil-");
     }    }
     /* printf("ii=%d", ij);    else 
        scanf("%d",i);*/      strcpy(digitp,"-stablbased-");
   imx=i-1; /* Number of individuals */  
     if (mobilav!=0) {
   /* for (i=1; i<=imx; i++){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     }*/      }
    /*  for (i=1; i<=imx; i++){    }
      if (s[4][i]==9)  s[4][i]=-1;  
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/    strcpy(fileresprobmorprev,"prmorprev"); 
      sprintf(digit,"%-d",ij);
      /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   /* Calculation of the number of parameter from char model*/    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   Tprod=ivector(1,15);    strcat(fileresprobmorprev,fileres);
   Tvaraff=ivector(1,15);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   Tvard=imatrix(1,15,1,2);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   Tage=ivector(1,15);            fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
        }
   if (strlen(model) >1){    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     j=0, j1=0, k1=1, k2=1;   
     j=nbocc(model,'+');    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     j1=nbocc(model,'*');    pstamp(ficresprobmorprev);
     cptcovn=j+1;    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);
     cptcovprod=j1;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
        for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     strcpy(modelsav,model);      fprintf(ficresprobmorprev," p.%-d SE",j);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      for(i=1; i<=nlstate;i++)
       printf("Error. Non available option model=%s ",model);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       fprintf(ficlog,"Error. Non available option model=%s ",model);    }  
       goto end;    fprintf(ficresprobmorprev,"\n");
     }    fprintf(ficgp,"\n# Routine varevsij");
        /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     for(i=(j+1); i>=1;i--){    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");
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */  /*   } */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       /*scanf("%d",i);*/    pstamp(ficresvij);
       if (strchr(strb,'*')) {  /* Model includes a product */    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/    if(popbased==1)
         if (strcmp(strc,"age")==0) { /* Vn*age */      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);
           cptcovprod--;    else
           cutv(strb,stre,strd,'V');      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/    fprintf(ficresvij,"# Age");
           cptcovage++;    for(i=1; i<=nlstate;i++)
             Tage[cptcovage]=i;      for(j=1; j<=nlstate;j++)
             /*printf("stre=%s ", stre);*/        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
         }    fprintf(ficresvij,"\n");
         else if (strcmp(strd,"age")==0) { /* or age*Vn */  
           cptcovprod--;    xp=vector(1,npar);
           cutv(strb,stre,strc,'V');    dnewm=matrix(1,nlstate,1,npar);
           Tvar[i]=atoi(stre);    doldm=matrix(1,nlstate,1,nlstate);
           cptcovage++;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           Tage[cptcovage]=i;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         }  
         else {  /* Age is not in the model */    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/    gpp=vector(nlstate+1,nlstate+ndeath);
           Tvar[i]=ncovcol+k1;    gmp=vector(nlstate+1,nlstate+ndeath);
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           Tprod[k1]=i;    
           Tvard[k1][1]=atoi(strc); /* m*/    if(estepm < stepm){
           Tvard[k1][2]=atoi(stre); /* n */      printf ("Problem %d lower than %d\n",estepm, stepm);
           Tvar[cptcovn+k2]=Tvard[k1][1];    }
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    else  hstepm=estepm;   
           for (k=1; k<=lastobs;k++)    /* For example we decided to compute the life expectancy with the smallest unit */
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           k1++;       nhstepm is the number of hstepm from age to agelim 
           k2=k2+2;       nstepm is the number of stepm from age to agelin. 
         }       Look at function hpijx to understand why (it is linked to memory size questions) */
       }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       else { /* no more sum */       survival function given by stepm (the optimization length). Unfortunately it
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/       means that if the survival funtion is printed every two years of age and if
        /*  scanf("%d",i);*/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       cutv(strd,strc,strb,'V');       results. So we changed our mind and took the option of the best precision.
       Tvar[i]=atoi(strc);    */
       }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       strcpy(modelsav,stra);      agelim = AGESUP;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         scanf("%d",i);*/      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     } /* end of loop + */      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   } /* end model */      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      gp=matrix(0,nhstepm,1,nlstate);
   printf("cptcovprod=%d ", cptcovprod);      gm=matrix(0,nhstepm,1,nlstate);
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/  
     fclose(fic);      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     /*  if(mle==1){*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     if (weightopt != 1) { /* Maximisation without weights*/        }
       for(i=1;i<=n;i++) weight[i]=1.0;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     /*-calculation of age at interview from date of interview and age at death -*/  
     agev=matrix(1,maxwav,1,imx);        if (popbased==1) {
           if(mobilav ==0){
     for (i=1; i<=imx; i++) {            for(i=1; i<=nlstate;i++)
       for(m=2; (m<= maxwav); m++) {              prlim[i][i]=probs[(int)age][i][ij];
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          }else{ /* mobilav */ 
          anint[m][i]=9999;            for(i=1; i<=nlstate;i++)
          s[m][i]=-1;              prlim[i][i]=mobaverage[(int)age][i][ij];
        }          }
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;        }
       }    
     }        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
     for (i=1; i<=imx; i++)  {            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       for(m=1; (m<= maxwav); m++){          }
         if(s[m][i] >0){        }
           if (s[m][i] >= nlstate+1) {        /* This for computing probability of death (h=1 means
             if(agedc[i]>0)           computed over hstepm matrices product = hstepm*stepm months) 
               if(moisdc[i]!=99 && andc[i]!=9999)           as a weighted average of prlim.
                 agev[m][i]=agedc[i];        */
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/        for(j=nlstate+1;j<=nlstate+ndeath;j++){
            else {          for(i=1,gpp[j]=0.; i<= nlstate; i++)
               if (andc[i]!=9999){            gpp[j] += prlim[i][i]*p3mat[i][j][1];
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        }    
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);        /* end probability of death */
               agev[m][i]=-1;  
               }        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
             }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           else if(s[m][i] !=9){ /* Should no more exist */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);   
             if(mint[m][i]==99 || anint[m][i]==9999)        if (popbased==1) {
               agev[m][i]=1;          if(mobilav ==0){
             else if(agev[m][i] <agemin){            for(i=1; i<=nlstate;i++)
               agemin=agev[m][i];              prlim[i][i]=probs[(int)age][i][ij];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          }else{ /* mobilav */ 
             }            for(i=1; i<=nlstate;i++)
             else if(agev[m][i] >agemax){              prlim[i][i]=mobaverage[(int)age][i][ij];
               agemax=agev[m][i];          }
              /* 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];*/        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
             /*   agev[m][i] = age[i]+2*m;*/          for(h=0; h<=nhstepm; h++){
           }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
           else { /* =9 */              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
             agev[m][i]=1;          }
             s[m][i]=-1;        }
           }        /* This for computing probability of death (h=1 means
         }           computed over hstepm matrices product = hstepm*stepm months) 
         else /*= 0 Unknown */           as a weighted average of prlim.
           agev[m][i]=1;        */
       }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
              for(i=1,gmp[j]=0.; i<= nlstate; i++)
     }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     for (i=1; i<=imx; i++)  {        }    
       for(m=1; (m<= maxwav); m++){        /* end probability of death */
         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);          for(j=1; j<= nlstate; j++) /* vareij */
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);            for(h=0; h<=nhstepm; h++){
           goto end;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         }          }
       }  
     }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
 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);  
       } /* End theta */
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);      for(h=0; h<=nhstepm; h++) /* veij */
     /* free_matrix(mint,1,maxwav,1,n);        for(j=1; j<=nlstate;j++)
        free_matrix(anint,1,maxwav,1,n);*/          for(theta=1; theta <=npar; theta++)
     free_vector(moisdc,1,n);            trgradg[h][j][theta]=gradg[h][theta][j];
     free_vector(andc,1,n);  
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
            for(theta=1; theta <=npar; theta++)
     wav=ivector(1,imx);          trgradgp[j][theta]=gradgp[theta][j];
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
          hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     /* Concatenates waves */      for(i=1;i<=nlstate;i++)
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       Tcode=ivector(1,100);      for(h=0;h<=nhstepm;h++){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        for(k=0;k<=nhstepm;k++){
       ncodemax[1]=1;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
                for(i=1;i<=nlstate;i++)
    codtab=imatrix(1,100,1,10);            for(j=1;j<=nlstate;j++)
    h=0;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
    m=pow(2,cptcoveff);        }
        }
    for(k=1;k<=cptcoveff; k++){    
      for(i=1; i <=(m/pow(2,k));i++){      /* pptj */
        for(j=1; j <= ncodemax[k]; j++){      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
            h++;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/          varppt[j][i]=doldmp[j][i];
          }      /* end ppptj */
        }      /*  x centered again */
      }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
    }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);   
       codtab[1][2]=1;codtab[2][2]=2; */      if (popbased==1) {
    /* for(i=1; i <=m ;i++){        if(mobilav ==0){
       for(k=1; k <=cptcovn; k++){          for(i=1; i<=nlstate;i++)
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);            prlim[i][i]=probs[(int)age][i][ij];
       }        }else{ /* mobilav */ 
       printf("\n");          for(i=1; i<=nlstate;i++)
       }            prlim[i][i]=mobaverage[(int)age][i][ij];
       scanf("%d",i);*/        }
          }
    /* Calculates basic frequencies. Computes observed prevalence at single age               
        and prints on file fileres'p'. */      /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
          */
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      }    
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      /* end probability of death */
        
     /* For Powell, parameters are in a vector p[] starting at p[1]      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
     if(mle==1){          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        }
     }      } 
          fprintf(ficresprobmorprev,"\n");
     /*--------- 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(ficresvij,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
    jk=1;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        }
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fprintf(ficresvij,"\n");
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      free_matrix(gp,0,nhstepm,1,nlstate);
    for(i=1,jk=1; i <=nlstate; i++){      free_matrix(gm,0,nhstepm,1,nlstate);
      for(k=1; k <=(nlstate+ndeath); k++){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
        if (k != i)      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
          {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            printf("%d%d ",i,k);    } /* End age */
            fprintf(ficlog,"%d%d ",i,k);    free_vector(gpp,nlstate+1,nlstate+ndeath);
            fprintf(ficres,"%1d%1d ",i,k);    free_vector(gmp,nlstate+1,nlstate+ndeath);
            for(j=1; j <=ncovmodel; j++){    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
              printf("%f ",p[jk]);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
              fprintf(ficlog,"%f ",p[jk]);    fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
              fprintf(ficres,"%f ",p[jk]);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
              jk++;    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("\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
            fprintf(ficlog,"\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
            fprintf(ficres,"\n");    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
          }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
      }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
    }    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
    if(mle==1){    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);
      /* Computing hessian and covariance matrix */    /*  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);
      ftolhess=ftol; /* Usually correct */  */
      hesscov(matcov, p, npar, delti, ftolhess, func);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
    }    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");  
    printf("# Scales (for hessian or gradient estimation)\n");    free_vector(xp,1,npar);
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");    free_matrix(doldm,1,nlstate,1,nlstate);
    for(i=1,jk=1; i <=nlstate; i++){    free_matrix(dnewm,1,nlstate,1,npar);
      for(j=1; j <=nlstate+ndeath; j++){    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        if (j!=i) {    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
          fprintf(ficres,"%1d%1d",i,j);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
          printf("%1d%1d",i,j);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
          fprintf(ficlog,"%1d%1d",i,j);    fclose(ficresprobmorprev);
          for(k=1; k<=ncovmodel;k++){    fflush(ficgp);
            printf(" %.5e",delti[jk]);    fflush(fichtm); 
            fprintf(ficlog," %.5e",delti[jk]);  }  /* end varevsij */
            fprintf(ficres," %.5e",delti[jk]);  
            jk++;  /************ Variance of prevlim ******************/
          }  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
          printf("\n");  {
          fprintf(ficlog,"\n");    /* Variance of prevalence limit */
          fprintf(ficres,"\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
        }  
      }    double **dnewm,**doldm;
    }    int i, j, nhstepm, hstepm;
        double *xp;
    k=1;    double *gp, *gm;
    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");    double **gradg, **trgradg;
    if(mle==1)    double age,agelim;
      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");    int theta;
    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++){    pstamp(ficresvpl);
      /*  if (k>nlstate) k=1;    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
          i1=(i-1)/(ncovmodel*nlstate)+1;    fprintf(ficresvpl,"# Age");
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    for(i=1; i<=nlstate;i++)
          printf("%s%d%d",alph[k],i1,tab[i]);*/        fprintf(ficresvpl," %1d-%1d",i,i);
      fprintf(ficres,"%3d",i);    fprintf(ficresvpl,"\n");
      if(mle==1)  
        printf("%3d",i);    xp=vector(1,npar);
      fprintf(ficlog,"%3d",i);    dnewm=matrix(1,nlstate,1,npar);
      for(j=1; j<=i;j++){    doldm=matrix(1,nlstate,1,nlstate);
        fprintf(ficres," %.5e",matcov[i][j]);    
        if(mle==1)    hstepm=1*YEARM; /* Every year of age */
          printf(" %.5e",matcov[i][j]);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
        fprintf(ficlog," %.5e",matcov[i][j]);    agelim = AGESUP;
      }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      fprintf(ficres,"\n");      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
      if(mle==1)      if (stepm >= YEARM) hstepm=1;
        printf("\n");      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
      fprintf(ficlog,"\n");      gradg=matrix(1,npar,1,nlstate);
      k++;      gp=vector(1,nlstate);
    }      gm=vector(1,nlstate);
      
    while((c=getc(ficpar))=='#' && c!= EOF){      for(theta=1; theta <=npar; theta++){
      ungetc(c,ficpar);        for(i=1; i<=npar; i++){ /* Computes gradient */
      fgets(line, MAXLINE, ficpar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
      puts(line);        }
      fputs(line,ficparo);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    }        for(i=1;i<=nlstate;i++)
    ungetc(c,ficpar);          gp[i] = prlim[i][i];
    estepm=0;      
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);        for(i=1; i<=npar; i++) /* Computes gradient */
    if (estepm==0 || estepm < stepm) estepm=stepm;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
    if (fage <= 2) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      bage = ageminpar;        for(i=1;i<=nlstate;i++)
      fage = agemaxpar;          gm[i] = prlim[i][i];
    }  
            for(i=1;i<=nlstate;i++)
    fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
    fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      } /* End theta */
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  
          trgradg =matrix(1,nlstate,1,npar);
    while((c=getc(ficpar))=='#' && c!= EOF){  
      ungetc(c,ficpar);      for(j=1; j<=nlstate;j++)
      fgets(line, MAXLINE, ficpar);        for(theta=1; theta <=npar; theta++)
      puts(line);          trgradg[j][theta]=gradg[theta][j];
      fputs(line,ficparo);  
    }      for(i=1;i<=nlstate;i++)
    ungetc(c,ficpar);        varpl[i][(int)age] =0.;
        matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      for(i=1;i<=nlstate;i++)
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
      
    while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficresvpl,"%.0f ",age );
      ungetc(c,ficpar);      for(i=1; i<=nlstate;i++)
      fgets(line, MAXLINE, ficpar);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
      puts(line);      fprintf(ficresvpl,"\n");
      fputs(line,ficparo);      free_vector(gp,1,nlstate);
    }      free_vector(gm,1,nlstate);
    ungetc(c,ficpar);      free_matrix(gradg,1,npar,1,nlstate);
        free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
    dateprev1=anprev1+mprev1/12.+jprev1/365.;  
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
   fscanf(ficpar,"pop_based=%d\n",&popbased);    free_matrix(dnewm,1,nlstate,1,nlstate);
   fprintf(ficparo,"pop_based=%d\n",popbased);    
   fprintf(ficres,"pop_based=%d\n",popbased);    }
    
   while((c=getc(ficpar))=='#' && c!= EOF){  /************ Variance of one-step probabilities  ******************/
     ungetc(c,ficpar);  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[])
     fgets(line, MAXLINE, ficpar);  {
     puts(line);    int i, j=0,  k1, l1, tj;
     fputs(line,ficparo);    int k2, l2, j1,  z1;
   }    int k=0, l;
   ungetc(c,ficpar);    int first=1, first1, first2;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   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);    double **dnewm,**doldm;
 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);    double *xp;
 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);    double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
 while((c=getc(ficpar))=='#' && c!= EOF){    double age, cov[NCOVMAX+1];
     ungetc(c,ficpar);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     fgets(line, MAXLINE, ficpar);    int theta;
     puts(line);    char fileresprob[FILENAMELENGTH];
     fputs(line,ficparo);    char fileresprobcov[FILENAMELENGTH];
   }    char fileresprobcor[FILENAMELENGTH];
   ungetc(c,ficpar);    double ***varpij;
   
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    strcpy(fileresprob,"prob"); 
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    strcat(fileresprob,fileres);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
 /*------------ gnuplot -------------*/    strcpy(fileresprobcov,"probcov"); 
   strcpy(optionfilegnuplot,optionfilefiname);    strcat(fileresprobcov,fileres);
   strcat(optionfilegnuplot,".gp");    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      printf("Problem with resultfile: %s\n", fileresprobcov);
     printf("Problem with file %s",optionfilegnuplot);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   }    }
   fclose(ficgp);    strcpy(fileresprobcor,"probcor"); 
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    strcat(fileresprobcor,fileres);
 /*--------- index.htm --------*/    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
   strcpy(optionfilehtm,optionfile);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   strcat(optionfilehtm,".htm");    }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Problem with %s \n",optionfilehtm), exit(0);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
 \n    pstamp(ficresprob);
 Total number of observations=%d <br>\n    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    fprintf(ficresprob,"# Age");
 <hr  size=\"2\" color=\"#EC5E5E\">    pstamp(ficresprobcov);
  <ul><li><h4>Parameter files</h4>\n    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    fprintf(ficresprobcov,"# Age");
  - Log file of the run: <a href=\"%s\">%s</a><br>\n    pstamp(ficresprobcor);
  - 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);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   fclose(fichtm);    fprintf(ficresprobcor,"# Age");
   
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);  
      for(i=1; i<=nlstate;i++)
 /*------------ free_vector  -------------*/      for(j=1; j<=(nlstate+ndeath);j++){
  chdir(path);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
          fprintf(ficresprobcov," p%1d-%1d ",i,j);
  free_ivector(wav,1,imx);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      }  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);     /* fprintf(ficresprob,"\n");
  free_ivector(num,1,n);    fprintf(ficresprobcov,"\n");
  free_vector(agedc,1,n);    fprintf(ficresprobcor,"\n");
  /*free_matrix(covar,1,NCOVMAX,1,n);*/   */
  fclose(ficparo);    xp=vector(1,npar);
  fclose(ficres);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   /*--------------- Prevalence limit --------------*/    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
      first=1;
   strcpy(filerespl,"pl");    fprintf(ficgp,"\n# Routine varprob");
   strcat(filerespl,fileres);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    fprintf(fichtm,"\n");
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
   }    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    file %s<br>\n",optionfilehtmcov);
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   fprintf(ficrespl,"#Prevalence limit\n");  and drawn. It helps understanding how is the covariance between two incidences.\
   fprintf(ficrespl,"#Age ");   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    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. \
   fprintf(ficrespl,"\n");  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
    would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   prlim=matrix(1,nlstate,1,nlstate);  standard deviations wide on each axis. <br>\
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    cov[1]=1;
   k=0;    /* tj=cptcoveff; */
   agebase=ageminpar;    tj = (int) pow(2,cptcoveff);
   agelim=agemaxpar;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   ftolpl=1.e-10;    j1=0;
   i1=cptcoveff;    for(j1=1; j1<=tj;j1++){
   if (cptcovn < 1){i1=1;}      /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
   for(cptcov=1;cptcov<=i1;cptcov++){        if  (cptcovn>0) {
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficresprob, "\n#********** Variable "); 
         k=k+1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          fprintf(ficresprob, "**********\n#\n");
         fprintf(ficrespl,"\n#******");          fprintf(ficresprobcov, "\n#********** Variable "); 
         printf("\n#******");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficlog,"\n#******");          fprintf(ficresprobcov, "**********\n#\n");
         for(j=1;j<=cptcoveff;j++) {          
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp, "\n#********** Variable "); 
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp, "**********\n#\n");
         }          
         fprintf(ficrespl,"******\n");          
         printf("******\n");          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
         fprintf(ficlog,"******\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                  fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
         for (age=agebase; age<=agelim; age++){          
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          fprintf(ficresprobcor, "\n#********** Variable ");    
           fprintf(ficrespl,"%.0f",age );          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for(i=1; i<=nlstate;i++)          fprintf(ficresprobcor, "**********\n#");    
           fprintf(ficrespl," %.5f", prlim[i][i]);        }
           fprintf(ficrespl,"\n");        
         }        gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       }        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     }        gp=vector(1,(nlstate)*(nlstate+ndeath));
   fclose(ficrespl);        gm=vector(1,(nlstate)*(nlstate+ndeath));
         for (age=bage; age<=fage; age ++){ 
   /*------------- h Pij x at various ages ------------*/          cov[2]=age;
            for (k=1; k<=cptcovn;k++) {
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                                                           * 1  1 1 1 1
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                                                           * 2  2 1 1 1
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;                                                           * 3  1 2 1 1
   }                                                           */
   printf("Computing pij: result on file '%s' \n", filerespij);            /* nbcode[1][1]=0 nbcode[1][2]=1;*/
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);          }
            for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for (k=1; k<=cptcovprod;k++)
   /*if (stepm<=24) stepsize=2;*/            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
   agelim=AGESUP;      
   hstepm=stepsize*YEARM; /* Every year of age */          for(theta=1; theta <=npar; theta++){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   /* hstepm=1;   aff par mois*/            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
   k=0;            
   for(cptcov=1;cptcov<=i1;cptcov++){            k=0;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            for(i=1; i<= (nlstate); i++){
       k=k+1;              for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficrespij,"\n#****** ");                k=k+1;
         for(j=1;j<=cptcoveff;j++)                gp[k]=pmmij[i][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 */            for(i=1; i<=npar; i++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
           /*      nhstepm=nhstepm*YEARM; aff par mois*/            k=0;
             for(i=1; i<=(nlstate); i++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              for(j=1; j<=(nlstate+ndeath);j++){
           oldm=oldms;savm=savms;                k=k+1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  gm[k]=pmmij[i][j];
           fprintf(ficrespij,"# Age");              }
           for(i=1; i<=nlstate;i++)            }
             for(j=1; j<=nlstate+ndeath;j++)       
               fprintf(ficrespij," %1d-%1d",i,j);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
           fprintf(ficrespij,"\n");              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
            for (h=0; h<=nhstepm; h++){          }
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
               for(j=1; j<=nlstate+ndeath;j++)            for(theta=1; theta <=npar; theta++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);              trgradg[j][theta]=gradg[theta][j];
             fprintf(ficrespij,"\n");          
              }          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           fprintf(ficrespij,"\n");  
         }          pmij(pmmij,cov,ncovmodel,x,nlstate);
     }          
   }          k=0;
           for(i=1; i<=(nlstate); i++){
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);            for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
   fclose(ficrespij);              mu[k][(int) age]=pmmij[i][j];
             }
           }
   /*---------- Forecasting ------------------*/          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   if((stepm == 1) && (strcmp(model,".")==0)){            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);              varpij[i][j][(int)age] = doldm[i][j];
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  
   }          /*printf("\n%d ",(int)age);
   else{            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     erreur=108;            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);            }*/
   }  
            fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
   /*---------- Health expectancies and variances ------------*/          fprintf(ficresprobcor,"\n%d ",(int)age);
   
   strcpy(filerest,"t");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   strcat(filerest,fileres);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   if((ficrest=fopen(filerest,"w"))==NULL) {          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   }          }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          i=0;
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);          for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
   strcpy(filerese,"e");              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   strcat(filerese,fileres);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   if((ficreseij=fopen(filerese,"w"))==NULL) {              for (j=1; j<=i;j++){
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                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]));
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);              }
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);            }
           }/* end of loop for state */
   strcpy(fileresv,"v");        } /* end of loop for age */
   strcat(fileresv,fileres);        free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);        free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   }        
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        /* Confidence intervalle of pij  */
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        /*
   calagedate=-1;          fprintf(ficgp,"\nunset parametric;unset label");
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          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");
   k=0;          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);
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       k=k+1;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       fprintf(ficrest,"\n#****** ");        */
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       fprintf(ficrest,"******\n");        first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
       fprintf(ficreseij,"\n#****** ");          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       for(j=1;j<=cptcoveff;j++)            if(l2==k2) continue;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            j=(k2-1)*(nlstate+ndeath)+l2;
       fprintf(ficreseij,"******\n");            for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       fprintf(ficresvij,"\n#****** ");                if(l1==k1) continue;
       for(j=1;j<=cptcoveff;j++)                i=(k1-1)*(nlstate+ndeath)+l1;
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                if(i<=j) continue;
       fprintf(ficresvij,"******\n");                for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
       oldm=oldms;savm=savms;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);                      cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                      mu1=mu[i][(int) age]/stepm*YEARM ;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                    mu2=mu[j][(int) age]/stepm*YEARM;
       oldm=oldms;savm=savms;                    c12=cv12/sqrt(v1*v2);
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);                    /* Computing eigen value of matrix of covariance */
       if(popbased==1){                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
        }                    if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                          first1=0;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                      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);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                      }
       fprintf(ficrest,"\n");                      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 */
       epj=vector(1,nlstate+1);                      /* lc2=fabs(lc2); */
       for(age=bage; age <=fage ;age++){                    }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
         if (popbased==1) {                    /* Eigen vectors */
           for(i=1; i<=nlstate;i++)                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
             prlim[i][i]=probs[(int)age][i][k];                    /*v21=sqrt(1.-v11*v11); *//* error */
         }                    v21=(lc1-v1)/cv12*v11;
                            v12=-v21;
         fprintf(ficrest," %4.0f",age);                    v22=v11;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                    tnalp=v21/v11;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                    if(first1==1){
             epj[j] += prlim[i][i]*eij[i][j][(int)age];                      first1=0;
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                      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);
           }                    }
           epj[nlstate+1] +=epj[j];                    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) */
         for(i=1, vepp=0.;i <=nlstate;i++)                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
           for(j=1;j <=nlstate;j++)                    if(first==1){
             vepp += vareij[i][j][(int)age];                      first=0;
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));                      fprintf(ficgp,"\nset parametric;unset label");
         for(j=1;j <=nlstate;j++){                      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(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));                      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>\
         fprintf(ficrest,"\n");   :<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);
 free_matrix(mint,1,maxwav,1,n);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     free_vector(weight,1,n);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   fclose(ficreseij);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   fclose(ficresvij);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   fclose(ficrest);                      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",\
   fclose(ficpar);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   free_vector(epj,1,nlstate+1);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                      }else{
   /*------- Variance limit prevalence------*/                        first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
   strcpy(fileresvpl,"vpl");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   strcat(fileresvpl,fileres);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                      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",\
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     exit(0);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   }                    }/* if first */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                  } /* age mod 5 */
                 } /* end loop age */
   k=0;                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   for(cptcov=1;cptcov<=i1;cptcov++){                first=1;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              } /*l12 */
       k=k+1;            } /* k12 */
       fprintf(ficresvpl,"\n#****** ");          } /*l1 */
       for(j=1;j<=cptcoveff;j++)        }/* k1 */
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        /* } /* loop covariates */
       fprintf(ficresvpl,"******\n");    }
          free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
       oldm=oldms;savm=savms;    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     }    free_vector(xp,1,npar);
  }    fclose(ficresprob);
     fclose(ficresprobcov);
   fclose(ficresvpl);    fclose(ficresprobcor);
     fflush(ficgp);
   /*---------- End : free ----------------*/    fflush(fichtmcov);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  }
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  /******************* Printing html file ***********/
    void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                      int lastpass, int stepm, int weightopt, char model[],\
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);                    int popforecast, int estepm ,\
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);                    double jprev1, double mprev1,double anprev1, \
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                    double jprev2, double mprev2,double anprev2){
      int jj1, k1, i1, cpt;
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
   free_matrix(agev,1,maxwav,1,imx);     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
   fprintf(fichtm,"\n</body>");   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
   fclose(fichtm);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
   fclose(ficgp);     fprintf(fichtm,"\
     - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
   if(erreur >0){     fprintf(fichtm,"\
     printf("End of Imach with error or warning %d\n",erreur);   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
   }else{     fprintf(fichtm,"\
    printf("End of Imach\n");   - (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): \
    fprintf(ficlog,"End of Imach\n");     <a href=\"%s\">%s</a> <br>\n",
   }             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   printf("See log file on %s\n",filelog);     fprintf(fichtm,"\
   fclose(ficlog);   - Population projections by age and states: \
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
    
   /* 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);*/  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   /*printf("Total time was %d uSec.\n", total_usecs);*/  
   /*------ End -----------*/   m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
  end:   jj1=0;
 #ifdef windows   for(k1=1; k1<=m;k1++){
   /* chdir(pathcd);*/     for(i1=1; i1<=ncodemax[k1];i1++){
 #endif       jj1++;
  /*system("wgnuplot graph.plt");*/       if (cptcovn > 0) {
  /*system("../gp37mgw/wgnuplot graph.plt");*/         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
  /*system("cd ../gp37mgw");*/         for (cpt=1; cpt<=cptcoveff;cpt++) 
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
  strcpy(plotcmd,GNUPLOTPROGRAM);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
  strcat(plotcmd," ");       }
  strcat(plotcmd,optionfilegnuplot);       /* Pij */
  system(plotcmd);       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);     
 #ifdef windows       /* Quasi-incidences */
   while (z[0] != 'q') {       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
     /* chdir(path); */   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> \
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");  <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
     scanf("%s",z);         /* Period (stable) prevalence in each health state */
     if (z[0] == 'c') system("./imach");         for(cpt=1; cpt<=nlstate;cpt++){
     else if (z[0] == 'e') system(optionfilehtm);           fprintf(fichtm,"<br>- Convergence from cross-sectional prevalence in each state (1 to %d) to period (stable) prevalence in specific state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
     else if (z[0] == 'g') system(plotcmd);  <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
     else if (z[0] == 'q') exit(0);         }
   }       for(cpt=1; cpt<=nlstate;cpt++) {
 #endif          fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
 }  <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         k=3;
         fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f]  ", ageminpar, agemaxpar);
         for (i=1; i<= nlstate ; i ++){
           if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
           else
             fprintf(ficgp,", '' ");
           l=(nlstate+ndeath)*(i-1)+1;
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
           for (j=1; j<= (nlstate-1) ; j ++)
             fprintf(ficgp,"+$%d",k+l+j);
           fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
         } /* nlstate */
         fprintf(ficgp,"\n");
       } /* end cpt state*/ 
     } /* end covariate */  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    /* avoid: */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32];
     int i,j, k, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
   
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i=0, j=0, n=0;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[MAXLINE], strb[MAXLINE];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       strcpy(line, linetmp);
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     /* endread: */
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int  j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     /*endread:*/
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
    /* endread:*/
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   
     int jj, ll, li, lj, lk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   
     char line[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int c,  h , cpt;
     int jl;
     int i1, j1, jk, stepsize;
     int *tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage=0, fage=110, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
   
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c";
   
     /*char  *strt;*/
     char strtend[80];
   
   
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
     curr_time=start_time;
     /*tml = *localtime(&start_time.tm_sec);*/
     /* strcpy(strstart,asctime(&tml)); */
     strcpy(strstart,asctime(&start_time));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tm_sec = tp.tm_sec +86400; */
   /*  tm = *localtime(&start_time.tm_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tm_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ( (i1-i) * (j1-j) != 0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #else
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #else
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    /* endfree:*/
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.51  
changed lines
  Added in v.1.164


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