Diff for /imach/src/imach.c between versions 1.50 and 1.160

version 1.50, 2002/06/26 23:25:02 version 1.160, 2014/09/02 09:24:05
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.160  2014/09/02 09:24:05  brouard
      *** empty log message ***
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.159  2014/09/01 10:34:10  brouard
   first survey ("cross") where individuals from different ages are    Summary: WIN32
   interviewed on their health status or degree of disability (in the    Author: Brouard
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.158  2014/08/27 17:11:51  brouard
   (if any) in individual health status.  Health expectancies are    *** empty log message ***
   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    Revision 1.157  2014/08/27 16:26:55  brouard
   Maximum Likelihood of the parameters involved in the model.  The    Summary: Preparing windows Visual studio version
   simplest model is the multinomial logistic model where pij is the    Author: Brouard
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    In order to compile on Visual studio, time.h is now correct and time_t
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    and tm struct should be used. difftime should be used but sometimes I
   'age' is age and 'sex' is a covariate. If you want to have a more    just make the differences in raw time format (time(&now).
   complex model than "constant and age", you should modify the program    Trying to suppress #ifdef LINUX
   where the markup *Covariates have to be included here again* invites    Add xdg-open for __linux in order to open default browser.
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.156  2014/08/25 20:10:10  brouard
     *** empty log message ***
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.155  2014/08/25 18:32:34  brouard
   identical for each individual. Also, if a individual missed an    Summary: New compile, minor changes
   intermediate interview, the information is lost, but taken into    Author: Brouard
   account using an interpolation or extrapolation.    
     Revision 1.154  2014/06/20 17:32:08  brouard
   hPijx is the probability to be observed in state i at age x+h    Summary: Outputs now all graphs of convergence to period prevalence
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.153  2014/06/20 16:45:46  brouard
   states. This elementary transition (by month or quarter trimester,    Summary: If 3 live state, convergence to period prevalence on same graph
   semester or year) is model as a multinomial logistic.  The hPx    Author: Brouard
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.152  2014/06/18 17:54:09  brouard
   hPijx.    Summary: open browser, use gnuplot on same dir than imach if not found in the path
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.151  2014/06/18 16:43:30  brouard
   of the life expectancies. It also computes the prevalence limits.    *** empty log message ***
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.150  2014/06/18 16:42:35  brouard
            Institut national d'études démographiques, Paris.    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
   This software have been partly granted by Euro-REVES, a concerted action    Author: brouard
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.149  2014/06/18 15:51:14  brouard
   software can be distributed freely for non commercial use. Latest version    Summary: Some fixes in parameter files errors
   can be accessed at http://euroreves.ined.fr/imach .    Author: Nicolas Brouard
   **********************************************************************/  
      Revision 1.148  2014/06/17 17:38:48  brouard
 #include <math.h>    Summary: Nothing new
 #include <stdio.h>    Author: Brouard
 #include <stdlib.h>  
 #include <unistd.h>    Just a new packaging for OS/X version 0.98nS
   
 #define MAXLINE 256    Revision 1.147  2014/06/16 10:33:11  brouard
 #define GNUPLOTPROGRAM "gnuplot"    *** empty log message ***
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.146  2014/06/16 10:20:28  brouard
 /*#define DEBUG*/    Summary: Merge
 #define windows    Author: Brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Merge, before building revised version.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.145  2014/06/10 21:23:15  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Summary: Debugging with valgrind
     Author: Nicolas Brouard
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Lot of changes in order to output the results with some covariates
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    After the Edimburgh REVES conference 2014, it seems mandatory to
 #define NCOVMAX 8 /* Maximum number of covariates */    improve the code.
 #define MAXN 20000    No more memory valgrind error but a lot has to be done in order to
 #define YEARM 12. /* Number of months per year */    continue the work of splitting the code into subroutines.
 #define AGESUP 130    Also, decodemodel has been improved. Tricode is still not
 #define AGEBASE 40    optimal. nbcode should be improved. Documentation has been added in
 #ifdef windows    the source code.
 #define DIRSEPARATOR '\\'  
 #define ODIRSEPARATOR '/'    Revision 1.143  2014/01/26 09:45:38  brouard
 #else    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
 #define DIRSEPARATOR '/'  
 #define ODIRSEPARATOR '\\'    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #endif    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    Revision 1.142  2014/01/26 03:57:36  brouard
 int erreur; /* Error number */    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 int nvar;  
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.141  2014/01/26 02:42:01  brouard
 int ndeath=1; /* Number of dead states */    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.140  2011/09/02 10:37:54  brouard
     Summary: times.h is ok with mingw32 now.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.139  2010/06/14 07:50:17  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 int mle, weightopt;    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.138  2010/04/30 18:19:40  brouard
 double jmean; /* Mean space between 2 waves */    *** empty log message ***
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.137  2010/04/29 18:11:38  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    (Module): Checking covariates for more complex models
 FILE *ficlog;    than V1+V2. A lot of change to be done. Unstable.
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *ficresprobmorprev;    Revision 1.136  2010/04/26 20:30:53  brouard
 FILE *fichtm; /* Html File */    (Module): merging some libgsl code. Fixing computation
 FILE *ficreseij;    of likelione (using inter/intrapolation if mle = 0) in order to
 char filerese[FILENAMELENGTH];    get same likelihood as if mle=1.
 FILE  *ficresvij;    Some cleaning of code and comments added.
 char fileresv[FILENAMELENGTH];  
 FILE  *ficresvpl;    Revision 1.135  2009/10/29 15:33:14  brouard
 char fileresvpl[FILENAMELENGTH];    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 char title[MAXLINE];  
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    Revision 1.134  2009/10/29 13:18:53  brouard
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    Revision 1.133  2009/07/06 10:21:25  brouard
 char filelog[FILENAMELENGTH]; /* Log file */    just nforces
 char filerest[FILENAMELENGTH];  
 char fileregp[FILENAMELENGTH];    Revision 1.132  2009/07/06 08:22:05  brouard
 char popfile[FILENAMELENGTH];    Many tings
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Revision 1.131  2009/06/20 16:22:47  brouard
     Some dimensions resccaled
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.130  2009/05/26 06:44:34  brouard
 #define FTOL 1.0e-10    (Module): Max Covariate is now set to 20 instead of 8. A
     lot of cleaning with variables initialized to 0. Trying to make
 #define NRANSI    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 #define ITMAX 200  
     Revision 1.129  2007/08/31 13:49:27  lievre
 #define TOL 2.0e-4    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   
 #define CGOLD 0.3819660    Revision 1.128  2006/06/30 13:02:05  brouard
 #define ZEPS 1.0e-10    (Module): Clarifications on computing e.j
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.127  2006/04/28 18:11:50  brouard
 #define GOLD 1.618034    (Module): Yes the sum of survivors was wrong since
 #define GLIMIT 100.0    imach-114 because nhstepm was no more computed in the age
 #define TINY 1.0e-20    loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
 static double maxarg1,maxarg2;    compute health expectancies (without variances) in a first step
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    and then all the health expectancies with variances or standard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    deviation (needs data from the Hessian matrices) which slows the
      computation.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    In the future we should be able to stop the program is only health
 #define rint(a) floor(a+0.5)    expectancies and graph are needed without standard deviations.
   
 static double sqrarg;    Revision 1.126  2006/04/28 17:23:28  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (Module): Yes the sum of survivors was wrong since
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
 int imx;    Version 0.98h
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.125  2006/04/04 15:20:31  lievre
     Errors in calculation of health expectancies. Age was not initialized.
 int estepm;    Forecasting file added.
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
     Revision 1.124  2006/03/22 17:13:53  lievre
 int m,nb;    Parameters are printed with %lf instead of %f (more numbers after the comma).
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    The log-likelihood is printed in the log file
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.123  2006/03/20 10:52:43  brouard
 double dateintmean=0;    * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
 double *weight;  
 int **s; /* Status */    * imach.c (Module): Weights can have a decimal point as for
 double *agedc, **covar, idx;    English (a comma might work with a correct LC_NUMERIC environment,
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    1.
 double ftolhess; /* Tolerance for computing hessian */    Version 0.98g
   
 /**************** split *************************/    Revision 1.122  2006/03/20 09:45:41  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    (Module): Weights can have a decimal point as for
 {    English (a comma might work with a correct LC_NUMERIC environment,
    char *s;                             /* pointer */    otherwise the weight is truncated).
    int  l1, l2;                         /* length counters */    Modification of warning when the covariates values are not 0 or
     1.
    l1 = strlen( path );                 /* length of path */    Version 0.98g
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    Revision 1.121  2006/03/16 17:45:01  lievre
    if ( s == NULL ) {                   /* no directory, so use current */    * imach.c (Module): Comments concerning covariates added
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)  
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    * imach.c (Module): refinements in the computation of lli if
 #if     defined(__bsd__)                /* get current working directory */    status=-2 in order to have more reliable computation if stepm is
       extern char       *getwd( );    not 1 month. Version 0.98f
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.120  2006/03/16 15:10:38  lievre
 #else    (Module): refinements in the computation of lli if
       extern char       *getcwd( );    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.119  2006/03/15 17:42:26  brouard
          return( GLOCK_ERROR_GETCWD );    (Module): Bug if status = -2, the loglikelihood was
       }    computed as likelihood omitting the logarithm. Version O.98e
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.118  2006/03/14 18:20:07  brouard
       s++;                              /* after this, the filename */    (Module): varevsij Comments added explaining the second
       l2 = strlen( s );                 /* length of filename */    table of variances if popbased=1 .
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
       strcpy( name, s );                /* save file name */    (Module): Function pstamp added
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    (Module): Version 0.98d
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.117  2006/03/14 17:16:22  brouard
    l1 = strlen( dirc );                 /* length of directory */    (Module): varevsij Comments added explaining the second
 #ifdef windows    table of variances if popbased=1 .
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #else    (Module): Function pstamp added
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    (Module): Version 0.98d
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.116  2006/03/06 10:29:27  brouard
    s++;    (Module): Variance-covariance wrong links and
    strcpy(ext,s);                       /* save extension */    varian-covariance of ej. is needed (Saito).
    l1= strlen( name);  
    l2= strlen( s)+1;    Revision 1.115  2006/02/27 12:17:45  brouard
    strncpy( finame, name, l1-l2);    (Module): One freematrix added in mlikeli! 0.98c
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    Revision 1.114  2006/02/26 12:57:58  brouard
 }    (Module): Some improvements in processing parameter
     filename with strsep.
   
 /******************************************/    Revision 1.113  2006/02/24 14:20:24  brouard
     (Module): Memory leaks checks with valgrind and:
 void replace(char *s, char*t)    datafile was not closed, some imatrix were not freed and on matrix
 {    allocation too.
   int i;  
   int lg=20;    Revision 1.112  2006/01/30 09:55:26  brouard
   i=0;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.111  2006/01/25 20:38:18  brouard
     (s[i] = t[i]);    (Module): Lots of cleaning and bugs added (Gompertz)
     if (t[i]== '\\') s[i]='/';    (Module): Comments can be added in data file. Missing date values
   }    can be a simple dot '.'.
 }  
     Revision 1.110  2006/01/25 00:51:50  brouard
 int nbocc(char *s, char occ)    (Module): Lots of cleaning and bugs added (Gompertz)
 {  
   int i,j=0;    Revision 1.109  2006/01/24 19:37:15  brouard
   int lg=20;    (Module): Comments (lines starting with a #) are allowed in data.
   i=0;  
   lg=strlen(s);    Revision 1.108  2006/01/19 18:05:42  lievre
   for(i=0; i<= lg; i++) {    Gnuplot problem appeared...
   if  (s[i] == occ ) j++;    To be fixed
   }  
   return j;    Revision 1.107  2006/01/19 16:20:37  brouard
 }    Test existence of gnuplot in imach path
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.106  2006/01/19 13:24:36  brouard
 {    Some cleaning and links added in html output
   /* cuts string t into u and v where u is ended by char occ excluding it  
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    Revision 1.105  2006/01/05 20:23:19  lievre
      gives u="abcedf" and v="ghi2j" */    *** empty log message ***
   int i,lg,j,p=0;  
   i=0;    Revision 1.104  2005/09/30 16:11:43  lievre
   for(j=0; j<=strlen(t)-1; j++) {    (Module): sump fixed, loop imx fixed, and simplifications.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    (Module): If the status is missing at the last wave but we know
   }    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
   lg=strlen(t);    contributions to the likelihood is 1 - Prob of dying from last
   for(j=0; j<p; j++) {    health status (= 1-p13= p11+p12 in the easiest case of somebody in
     (u[j] = t[j]);    the healthy state at last known wave). Version is 0.98
   }  
      u[p]='\0';    Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Revision 1.102  2004/09/15 17:31:30  brouard
   }    Add the possibility to read data file including tab characters.
 }  
     Revision 1.101  2004/09/15 10:38:38  brouard
 /********************** nrerror ********************/    Fix on curr_time
   
 void nrerror(char error_text[])    Revision 1.100  2004/07/12 18:29:06  brouard
 {    Add version for Mac OS X. Just define UNIX in Makefile
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.99  2004/06/05 08:57:40  brouard
   exit(1);    *** empty log message ***
 }  
 /*********************** vector *******************/    Revision 1.98  2004/05/16 15:05:56  brouard
 double *vector(int nl, int nh)    New version 0.97 . First attempt to estimate force of mortality
 {    directly from the data i.e. without the need of knowing the health
   double *v;    state at each age, but using a Gompertz model: log u =a + b*age .
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    This is the basic analysis of mortality and should be done before any
   if (!v) nrerror("allocation failure in vector");    other analysis, in order to test if the mortality estimated from the
   return v-nl+NR_END;    cross-longitudinal survey is different from the mortality estimated
 }    from other sources like vital statistic data.
   
 /************************ free vector ******************/    The same imach parameter file can be used but the option for mle should be -3.
 void free_vector(double*v, int nl, int nh)  
 {    Agnès, who wrote this part of the code, tried to keep most of the
   free((FREE_ARG)(v+nl-NR_END));    former routines in order to include the new code within the former code.
 }  
     The output is very simple: only an estimate of the intercept and of
 /************************ivector *******************************/    the slope with 95% confident intervals.
 int *ivector(long nl,long nh)  
 {    Current limitations:
   int *v;    A) Even if you enter covariates, i.e. with the
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   if (!v) nrerror("allocation failure in ivector");    B) There is no computation of Life Expectancy nor Life Table.
   return v-nl+NR_END;  
 }    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
 /******************free ivector **************************/    suppressed.
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.96  2003/07/15 15:38:55  brouard
   free((FREE_ARG)(v+nl-NR_END));    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 }    rewritten within the same printf. Workaround: many printfs.
   
 /******************* imatrix *******************************/    Revision 1.95  2003/07/08 07:54:34  brouard
 int **imatrix(long nrl, long nrh, long ncl, long nch)    * imach.c (Repository):
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    (Repository): Using imachwizard code to output a more meaningful covariance
 {    matrix (cov(a12,c31) instead of numbers.
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    Revision 1.94  2003/06/27 13:00:02  brouard
      Just cleaning
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Revision 1.93  2003/06/25 16:33:55  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): On windows (cygwin) function asctime_r doesn't
   m += NR_END;    exist so I changed back to asctime which exists.
   m -= nrl;    (Module): Version 0.96b
    
      Revision 1.92  2003/06/25 16:30:45  brouard
   /* allocate rows and set pointers to them */    (Module): On windows (cygwin) function asctime_r doesn't
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    exist so I changed back to asctime which exists.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.91  2003/06/25 15:30:29  brouard
   m[nrl] -= ncl;    * imach.c (Repository): Duplicated warning errors corrected.
      (Repository): Elapsed time after each iteration is now output. It
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    helps to forecast when convergence will be reached. Elapsed time
      is stamped in powell.  We created a new html file for the graphs
   /* return pointer to array of pointers to rows */    concerning matrix of covariance. It has extension -cov.htm.
   return m;  
 }    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 /****************** free_imatrix *************************/    mle=-1 a template is output in file "or"mypar.txt with the design
 void free_imatrix(m,nrl,nrh,ncl,nch)    of the covariance matrix to be input.
       int **m;  
       long nch,ncl,nrh,nrl;    Revision 1.89  2003/06/24 12:30:52  brouard
      /* free an int matrix allocated by imatrix() */    (Module): Some bugs corrected for windows. Also, when
 {    mle=-1 a template is output in file "or"mypar.txt with the design
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    of the covariance matrix to be input.
   free((FREE_ARG) (m+nrl-NR_END));  
 }    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.
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Revision 1.87  2003/06/18 12:26:01  brouard
 {    Version 0.96
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    routine fileappend.
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Revision 1.85  2003/06/17 13:12:43  brouard
   m -= nrl;    * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    prior to the death. In this case, dh was negative and likelihood
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    was wrong (infinity). We still send an "Error" but patch by
   m[nrl] += NR_END;    assuming that the date of death was just one stepm after the
   m[nrl] -= ncl;    interview.
     (Repository): Because some people have very long ID (first column)
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    we changed int to long in num[] and we added a new lvector for
   return m;    memory allocation. But we also truncated to 8 characters (left
 }    truncation)
     (Repository): No more line truncation errors.
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    Revision 1.84  2003/06/13 21:44:43  brouard
 {    * imach.c (Repository): Replace "freqsummary" at a correct
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    place. It differs from routine "prevalence" which may be called
   free((FREE_ARG)(m+nrl-NR_END));    many times. Probs is memory consuming and must be used with
 }    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    Revision 1.83  2003/06/10 13:39:11  lievre
 {    *** empty log message ***
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;    Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  */
   m += NR_END;  /*
   m -= nrl;     Interpolated Markov Chain
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Short summary of the programme:
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    
   m[nrl] += NR_END;    This program computes Healthy Life Expectancies from
   m[nrl] -= ncl;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    second wave of interviews ("longitudinal") which measure each change
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    (if any) in individual health status.  Health expectancies are
   m[nrl][ncl] += NR_END;    computed from the time spent in each health state according to a
   m[nrl][ncl] -= nll;    model. More health states you consider, more time is necessary to reach the
   for (j=ncl+1; j<=nch; j++)    Maximum Likelihood of the parameters involved in the model.  The
     m[nrl][j]=m[nrl][j-1]+nlay;    simplest model is the multinomial logistic model where pij is the
      probability to be observed in state j at the second wave
   for (i=nrl+1; i<=nrh; i++) {    conditional to be observed in state i at the first wave. Therefore
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     for (j=ncl+1; j<=nch; j++)    'age' is age and 'sex' is a covariate. If you want to have a more
       m[i][j]=m[i][j-1]+nlay;    complex model than "constant and age", you should modify the program
   }    where the markup *Covariates have to be included here again* invites
   return m;    you to do it.  More covariates you add, slower the
 }    convergence.
   
 /*************************free ma3x ************************/    The advantage of this computer programme, compared to a simple
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    multinomial logistic model, is clear when the delay between waves is not
 {    identical for each individual. Also, if a individual missed an
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    intermediate interview, the information is lost, but taken into
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    account using an interpolation or extrapolation.  
   free((FREE_ARG)(m+nrl-NR_END));  
 }    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
 /***************** f1dim *************************/    split into an exact number (nh*stepm) of unobserved intermediate
 extern int ncom;    states. This elementary transition (by month, quarter,
 extern double *pcom,*xicom;    semester or year) is modelled as a multinomial logistic.  The hPx
 extern double (*nrfunc)(double []);    matrix is simply the matrix product of nh*stepm elementary matrices
      and the contribution of each individual to the likelihood is simply
 double f1dim(double x)    hPijx.
 {  
   int j;    Also this programme outputs the covariance matrix of the parameters but also
   double f;    of the life expectancies. It also computes the period (stable) prevalence. 
   double *xt;    
      Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   xt=vector(1,ncom);             Institut national d'études démographiques, Paris.
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    This software have been partly granted by Euro-REVES, a concerted action
   f=(*nrfunc)(xt);    from the European Union.
   free_vector(xt,1,ncom);    It is copyrighted identically to a GNU software product, ie programme and
   return f;    software can be distributed freely for non commercial use. Latest version
 }    can be accessed at http://euroreves.ined.fr/imach .
   
 /*****************brent *************************/    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 {    
   int iter;    **********************************************************************/
   double a,b,d,etemp;  /*
   double fu,fv,fw,fx;    main
   double ftemp;    read parameterfile
   double p,q,r,tol1,tol2,u,v,w,x,xm;    read datafile
   double e=0.0;    concatwav
      freqsummary
   a=(ax < cx ? ax : cx);    if (mle >= 1)
   b=(ax > cx ? ax : cx);      mlikeli
   x=w=v=bx;    print results files
   fw=fv=fx=(*f)(x);    if mle==1 
   for (iter=1;iter<=ITMAX;iter++) {       computes hessian
     xm=0.5*(a+b);    read end of parameter file: agemin, agemax, bage, fage, estepm
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);        begin-prev-date,...
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    open gnuplot file
     printf(".");fflush(stdout);    open html file
     fprintf(ficlog,".");fflush(ficlog);    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
 #ifdef DEBUG     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
     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);                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
     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);      freexexit2 possible for memory heap.
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif    h Pij x                         | pij_nom  ficrestpij
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
       *xmin=x;         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
       return fx;         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
     }  
     ftemp=fu;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
     if (fabs(e) > tol1) {         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
       r=(x-w)*(fx-fv);    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
       q=(x-v)*(fx-fw);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
       p=(x-v)*q-(x-w)*r;     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;    forecasting if prevfcast==1 prevforecast call prevalence()
       q=fabs(q);    health expectancies
       etemp=e;    Variance-covariance of DFLE
       e=d;    prevalence()
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))     movingaverage()
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    varevsij() 
       else {    if popbased==1 varevsij(,popbased)
         d=p/q;    total life expectancies
         u=x+d;    Variance of period (stable) prevalence
         if (u-a < tol2 || b-u < tol2)   end
           d=SIGN(tol1,xm-x);  */
       }  
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }   
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  #include <math.h>
     fu=(*f)(u);  #include <stdio.h>
     if (fu <= fx) {  #include <stdlib.h>
       if (u >= x) a=x; else b=x;  #include <string.h>
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  #ifdef _WIN32
         } else {  #include <io.h>
           if (u < x) a=u; else b=u;  #else
           if (fu <= fw || w == x) {  #include <unistd.h>
             v=w;  #endif
             w=u;  
             fv=fw;  #include <limits.h>
             fw=fu;  #include <sys/types.h>
           } else if (fu <= fv || v == x || v == w) {  #include <sys/stat.h>
             v=u;  #include <errno.h>
             fv=fu;  /* extern int errno; */
           }  
         }  /* #ifdef LINUX */
   }  /* #include <time.h> */
   nrerror("Too many iterations in brent");  /* #include "timeval.h" */
   *xmin=x;  /* #else */
   return fx;  /* #include <sys/time.h> */
 }  /* #endif */
   
 /****************** mnbrak ***********************/  #include <time.h>
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #ifdef GSL
             double (*func)(double))  #include <gsl/gsl_errno.h>
 {  #include <gsl/gsl_multimin.h>
   double ulim,u,r,q, dum;  #endif
   double fu;  
    /* #include <libintl.h> */
   *fa=(*func)(*ax);  /* #define _(String) gettext (String) */
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  #define GNUPLOTPROGRAM "gnuplot"
       }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   *cx=(*bx)+GOLD*(*bx-*ax);  #define FILENAMELENGTH 132
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
     r=(*bx-*ax)*(*fb-*fc);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {  #define NINTERVMAX 8
       fu=(*func)(u);  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
       fu=(*func)(u);  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
       if (fu < *fc) {  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  #define MAXN 20000
           SHFT(*fb,*fc,fu,(*func)(u))  #define YEARM 12. /**< Number of months per year */
           }  #define AGESUP 130
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  #define AGEBASE 40
       u=ulim;  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
       fu=(*func)(u);  #ifdef _WIN32
     } else {  #define DIRSEPARATOR '\\'
       u=(*cx)+GOLD*(*cx-*bx);  #define CHARSEPARATOR "\\"
       fu=(*func)(u);  #define ODIRSEPARATOR '/'
     }  #else
     SHFT(*ax,*bx,*cx,u)  #define DIRSEPARATOR '/'
       SHFT(*fa,*fb,*fc,fu)  #define CHARSEPARATOR "/"
       }  #define ODIRSEPARATOR '\\'
 }  #endif
   
 /*************** linmin ************************/  /* $Id$ */
   /* $State$ */
 int ncom;  
 double *pcom,*xicom;  char version[]="Imach version 0.98nX, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
 double (*nrfunc)(double []);  char fullversion[]="$Revision$ $Date$"; 
    char strstart[80];
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 {  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   double brent(double ax, double bx, double cx,  int nvar=0, nforce=0; /* Number of variables, number of forces */
                double (*f)(double), double tol, double *xmin);  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   double f1dim(double x);  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
               double *fc, double (*func)(double));  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
   int j;  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   double xx,xmin,bx,ax;  int cptcovprodnoage=0; /**< Number of covariate products without age */   
   double fx,fb,fa;  int cptcoveff=0; /* Total number of covariates to vary for printing results */
    int cptcov=0; /* Working variable */
   ncom=n;  int npar=NPARMAX;
   pcom=vector(1,n);  int nlstate=2; /* Number of live states */
   xicom=vector(1,n);  int ndeath=1; /* Number of dead states */
   nrfunc=func;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   for (j=1;j<=n;j++) {  int popbased=0;
     pcom[j]=p[j];  
     xicom[j]=xi[j];  int *wav; /* Number of waves for this individuual 0 is possible */
   }  int maxwav=0; /* Maxim number of waves */
   ax=0.0;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   xx=1.0;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);                     to the likelihood and the sum of weights (done by funcone)*/
 #ifdef DEBUG  int mle=1, weightopt=0;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 #endif  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   for (j=1;j<=n;j++) {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     xi[j] *= xmin;  double jmean=1; /* Mean space between 2 waves */
     p[j] += xi[j];  double **matprod2(); /* test */
   }  double **oldm, **newm, **savm; /* Working pointers to matrices */
   free_vector(xicom,1,n);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   free_vector(pcom,1,n);  /*FILE *fic ; */ /* Used in readdata only */
 }  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
 /*************** powell ************************/  int globpr=0; /* Global variable for printing or not */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  double fretone; /* Only one call to likelihood */
             double (*func)(double []))  long ipmx=0; /* Number of contributions */
 {  double sw; /* Sum of weights */
   void linmin(double p[], double xi[], int n, double *fret,  char filerespow[FILENAMELENGTH];
               double (*func)(double []));  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   int i,ibig,j;  FILE *ficresilk;
   double del,t,*pt,*ptt,*xit;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   double fp,fptt;  FILE *ficresprobmorprev;
   double *xits;  FILE *fichtm, *fichtmcov; /* Html File */
   pt=vector(1,n);  FILE *ficreseij;
   ptt=vector(1,n);  char filerese[FILENAMELENGTH];
   xit=vector(1,n);  FILE *ficresstdeij;
   xits=vector(1,n);  char fileresstde[FILENAMELENGTH];
   *fret=(*func)(p);  FILE *ficrescveij;
   for (j=1;j<=n;j++) pt[j]=p[j];  char filerescve[FILENAMELENGTH];
   for (*iter=1;;++(*iter)) {  FILE  *ficresvij;
     fp=(*fret);  char fileresv[FILENAMELENGTH];
     ibig=0;  FILE  *ficresvpl;
     del=0.0;  char fileresvpl[FILENAMELENGTH];
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  char title[MAXLINE];
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     for (i=1;i<=n;i++)  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       printf(" %d %.12f",i, p[i]);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     fprintf(ficlog," %d %.12f",i, p[i]);  char command[FILENAMELENGTH];
     printf("\n");  int  outcmd=0;
     fprintf(ficlog,"\n");  
     for (i=1;i<=n;i++) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  char filelog[FILENAMELENGTH]; /* Log file */
 #ifdef DEBUG  char filerest[FILENAMELENGTH];
       printf("fret=%lf \n",*fret);  char fileregp[FILENAMELENGTH];
       fprintf(ficlog,"fret=%lf \n",*fret);  char popfile[FILENAMELENGTH];
 #endif  
       printf("%d",i);fflush(stdout);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       fprintf(ficlog,"%d",i);fflush(ficlog);  
       linmin(p,xit,n,fret,func);  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
       if (fabs(fptt-(*fret)) > del) {  /* struct timezone tzp; */
         del=fabs(fptt-(*fret));  /* extern int gettimeofday(); */
         ibig=i;  struct tm tml, *gmtime(), *localtime();
       }  
 #ifdef DEBUG  extern time_t time();
       printf("%d %.12e",i,(*fret));  
       fprintf(ficlog,"%d %.12e",i,(*fret));  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 */
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  struct tm tm;
         printf(" x(%d)=%.12e",j,xit[j]);  
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  char strcurr[80], strfor[80];
       }  
       for(j=1;j<=n;j++) {  char *endptr;
         printf(" p=%.12e",p[j]);  long lval;
         fprintf(ficlog," p=%.12e",p[j]);  double dval;
       }  
       printf("\n");  #define NR_END 1
       fprintf(ficlog,"\n");  #define FREE_ARG char*
 #endif  #define FTOL 1.0e-10
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #define NRANSI 
 #ifdef DEBUG  #define ITMAX 200 
       int k[2],l;  
       k[0]=1;  #define TOL 2.0e-4 
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  #define CGOLD 0.3819660 
       fprintf(ficlog,"Max: %.12e",(*func)(p));  #define ZEPS 1.0e-10 
       for (j=1;j<=n;j++) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
         printf(" %.12e",p[j]);  
         fprintf(ficlog," %.12e",p[j]);  #define GOLD 1.618034 
       }  #define GLIMIT 100.0 
       printf("\n");  #define TINY 1.0e-20 
       fprintf(ficlog,"\n");  
       for(l=0;l<=1;l++) {  static double maxarg1,maxarg2;
         for (j=1;j<=n;j++) {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
           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]);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
         }  #define rint(a) floor(a+0.5)
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  static double sqrarg;
       }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #endif  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int agegomp= AGEGOMP;
   
       free_vector(xit,1,n);  int imx; 
       free_vector(xits,1,n);  int stepm=1;
       free_vector(ptt,1,n);  /* Stepm, step in month: minimum step interpolation*/
       free_vector(pt,1,n);  
       return;  int estepm;
     }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {  int m,nb;
       ptt[j]=2.0*p[j]-pt[j];  long *num;
       xit[j]=p[j]-pt[j];  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       pt[j]=p[j];  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     }  double **pmmij, ***probs;
     fptt=(*func)(ptt);  double *ageexmed,*agecens;
     if (fptt < fp) {  double dateintmean=0;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {  double *weight;
         linmin(p,xit,n,fret,func);  int **s; /* Status */
         for (j=1;j<=n;j++) {  double *agedc;
           xi[j][ibig]=xi[j][n];  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
           xi[j][n]=xit[j];                    * covar=matrix(0,NCOVMAX,1,n); 
         }                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
 #ifdef DEBUG  double  idx; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int *Ndum; /** Freq of modality (tricode */
         for(j=1;j<=n;j++){  int **codtab; /**< codtab=imatrix(1,100,1,10); */
           printf(" %.12e",xit[j]);  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
           fprintf(ficlog," %.12e",xit[j]);  double *lsurv, *lpop, *tpop;
         }  
         printf("\n");  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
         fprintf(ficlog,"\n");  double ftolhess; /**< Tolerance for computing hessian */
 #endif  
       }  /**************** split *************************/
     }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   }  {
 }    /* 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)
 /**** Prevalence limit ****************/    */ 
     char  *ss;                            /* pointer */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    int   l1, l2;                         /* length counters */
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    l1 = strlen(path );                   /* length of path */
      matrix by transitions matrix until convergence is reached */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   int i, ii,j,k;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   double min, max, maxmin, maxmax,sumnew=0.;      strcpy( name, path );               /* we got the fullname name because no directory */
   double **matprod2();      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   double **out, cov[NCOVMAX], **pmij();        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   double **newm;      /* get current working directory */
   double agefin, delaymax=50 ; /* Max number of years to converge */      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   for (ii=1;ii<=nlstate+ndeath;ii++)        return( GLOCK_ERROR_GETCWD );
     for (j=1;j<=nlstate+ndeath;j++){      }
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      /* got dirc from getcwd*/
     }      printf(" DIRC = %s \n",dirc);
     } else {                              /* strip direcotry from path */
    cov[1]=1.;      ss++;                               /* after this, the filename */
        l2 = strlen( ss );                  /* length of filename */
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      strcpy( name, ss );         /* save file name */
     newm=savm;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     /* Covariates have to be included here again */      dirc[l1-l2] = 0;                    /* add zero */
      cov[2]=agefin;      printf(" DIRC2 = %s \n",dirc);
      }
       for (k=1; k<=cptcovn;k++) {    /* We add a separator at the end of dirc if not exists */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    l1 = strlen( dirc );                  /* length of directory */
         /*      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]]);*/    if( dirc[l1-1] != DIRSEPARATOR ){
       }      dirc[l1] =  DIRSEPARATOR;
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      dirc[l1+1] = 0; 
       for (k=1; k<=cptcovprod;k++)      printf(" DIRC3 = %s \n",dirc);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    }
     ss = strrchr( name, '.' );            /* find last / */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    if (ss >0){
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      ss++;
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      strcpy(ext,ss);                     /* save extension */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      l1= strlen( name);
       l2= strlen(ss)+1;
     savm=oldm;      strncpy( finame, name, l1-l2);
     oldm=newm;      finame[l1-l2]= 0;
     maxmax=0.;    }
     for(j=1;j<=nlstate;j++){  
       min=1.;    return( 0 );                          /* we're done */
       max=0.;  }
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  /******************************************/
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  void replace_back_to_slash(char *s, char*t)
         min=FMIN(min,prlim[i][j]);  {
       }    int i;
       maxmin=max-min;    int lg=0;
       maxmax=FMAX(maxmax,maxmin);    i=0;
     }    lg=strlen(t);
     if(maxmax < ftolpl){    for(i=0; i<= lg; i++) {
       return prlim;      (s[i] = t[i]);
     }      if (t[i]== '\\') s[i]='/';
   }    }
 }  }
   
 /*************** transition probabilities ***************/  char *trimbb(char *out, char *in)
   { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    char *s;
 {    s=out;
   double s1, s2;    while (*in != '\0'){
   /*double t34;*/      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   int i,j,j1, nc, ii, jj;        in++;
       }
     for(i=1; i<= nlstate; i++){      *out++ = *in++;
     for(j=1; j<i;j++){    }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    *out='\0';
         /*s2 += param[i][j][nc]*cov[nc];*/    return s;
         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);*/  
       }  char *cutl(char *blocc, char *alocc, char *in, char occ)
       ps[i][j]=s2;  {
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
     }       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     for(j=i+1; j<=nlstate+ndeath;j++){       gives blocc="abcdef2ghi" and alocc="j".
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){       If occ is not found blocc is null and alocc is equal to in. Returns blocc
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    char *s, *t;
       }    t=in;s=in;
       ps[i][j]=s2;    while ((*in != occ) && (*in != '\0')){
     }      *alocc++ = *in++;
   }    }
     /*ps[3][2]=1;*/    if( *in == occ){
       *(alocc)='\0';
   for(i=1; i<= nlstate; i++){      s=++in;
      s1=0;    }
     for(j=1; j<i; j++)   
       s1+=exp(ps[i][j]);    if (s == t) {/* occ not found */
     for(j=i+1; j<=nlstate+ndeath; j++)      *(alocc-(in-s))='\0';
       s1+=exp(ps[i][j]);      in=s;
     ps[i][i]=1./(s1+1.);    }
     for(j=1; j<i; j++)    while ( *in != '\0'){
       ps[i][j]= exp(ps[i][j])*ps[i][i];      *blocc++ = *in++;
     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 */    *blocc='\0';
   } /* end i */    return t;
   }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  char *cutv(char *blocc, char *alocc, char *in, char occ)
     for(jj=1; jj<= nlstate+ndeath; jj++){  {
       ps[ii][jj]=0;    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
       ps[ii][ii]=1;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     }       gives blocc="abcdef2ghi" and alocc="j".
   }       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     */
     char *s, *t;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    t=in;s=in;
     for(jj=1; jj<= nlstate+ndeath; jj++){    while (*in != '\0'){
      printf("%lf ",ps[ii][jj]);      while( *in == occ){
    }        *blocc++ = *in++;
     printf("\n ");        s=in;
     }      }
     printf("\n ");printf("%lf ",cov[2]);*/      *blocc++ = *in++;
 /*    }
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    if (s == t) /* occ not found */
   goto end;*/      *(blocc-(in-s))='\0';
     return ps;    else
 }      *(blocc-(in-s)-1)='\0';
     in=s;
 /**************** Product of 2 matrices ******************/    while ( *in != '\0'){
       *alocc++ = *in++;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    }
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    *alocc='\0';
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    return s;
   /* in, b, out are matrice of pointers which should have been initialized  }
      before: only the contents of out is modified. The function returns  
      a pointer to pointers identical to out */  int nbocc(char *s, char occ)
   long i, j, k;  {
   for(i=nrl; i<= nrh; i++)    int i,j=0;
     for(k=ncolol; k<=ncoloh; k++)    int lg=20;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    i=0;
         out[i][k] +=in[i][j]*b[j][k];    lg=strlen(s);
     for(i=0; i<= lg; i++) {
   return out;    if  (s[i] == occ ) j++;
 }    }
     return j;
   }
 /************* Higher Matrix Product ***************/  
   /* void cutv(char *u,char *v, char*t, char occ) */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  /* { */
 {  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
      duration (i.e. until  /*      gives u="abcdef2ghi" and v="j" *\/ */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  /*   int i,lg,j,p=0; */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  /*   i=0; */
      (typically every 2 years instead of every month which is too big).  /*   lg=strlen(t); */
      Model is determined by parameters x and covariates have to be  /*   for(j=0; j<=lg-1; j++) { */
      included manually here.  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   /*   } */
      */  
   /*   for(j=0; j<p; j++) { */
   int i, j, d, h, k;  /*     (u[j] = t[j]); */
   double **out, cov[NCOVMAX];  /*   } */
   double **newm;  /*      u[p]='\0'; */
   
   /* Hstepm could be zero and should return the unit matrix */  /*    for(j=0; j<= lg; j++) { */
   for (i=1;i<=nlstate+ndeath;i++)  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
     for (j=1;j<=nlstate+ndeath;j++){  /*   } */
       oldm[i][j]=(i==j ? 1.0 : 0.0);  /* } */
       po[i][j][0]=(i==j ? 1.0 : 0.0);  
     }  #ifdef _WIN32
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  char * strsep(char **pp, const char *delim)
   for(h=1; h <=nhstepm; h++){  {
     for(d=1; d <=hstepm; d++){    char *p, *q;
       newm=savm;           
       /* Covariates have to be included here again */    if ((p = *pp) == NULL)
       cov[1]=1.;      return 0;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    if ((q = strpbrk (p, delim)) != NULL)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    {
       for (k=1; k<=cptcovage;k++)      *pp = q + 1;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      *q = '\0';
       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]]];    else
       *pp = 0;
     return p;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  }
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  #endif
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  /********************** nrerror ********************/
       savm=oldm;  
       oldm=newm;  void nrerror(char error_text[])
     }  {
     for(i=1; i<=nlstate+ndeath; i++)    fprintf(stderr,"ERREUR ...\n");
       for(j=1;j<=nlstate+ndeath;j++) {    fprintf(stderr,"%s\n",error_text);
         po[i][j][h]=newm[i][j];    exit(EXIT_FAILURE);
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  }
          */  /*********************** vector *******************/
       }  double *vector(int nl, int nh)
   } /* end h */  {
   return po;    double *v;
 }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
 /*************** log-likelihood *************/  }
 double func( double *x)  
 {  /************************ free vector ******************/
   int i, ii, j, k, mi, d, kk;  void free_vector(double*v, int nl, int nh)
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  {
   double **out;    free((FREE_ARG)(v+nl-NR_END));
   double sw; /* Sum of weights */  }
   double lli; /* Individual log likelihood */  
   long ipmx;  /************************ivector *******************************/
   /*extern weight */  int *ivector(long nl,long nh)
   /* We are differentiating ll according to initial status */  {
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    int *v;
   /*for(i=1;i<imx;i++)    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     printf(" %d\n",s[4][i]);    if (!v) nrerror("allocation failure in ivector");
   */    return v-nl+NR_END;
   cov[1]=1.;  }
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;  /******************free ivector **************************/
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  void free_ivector(int *v, long nl, long nh)
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  {
     for(mi=1; mi<= wav[i]-1; mi++){    free((FREE_ARG)(v+nl-NR_END));
       for (ii=1;ii<=nlstate+ndeath;ii++)  }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
       for(d=0; d<dh[mi][i]; d++){  /************************lvector *******************************/
         newm=savm;  long *lvector(long nl,long nh)
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  {
         for (kk=1; kk<=cptcovage;kk++) {    long *v;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         }    if (!v) nrerror("allocation failure in ivector");
            return v-nl+NR_END;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  }
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
         savm=oldm;  /******************free lvector **************************/
         oldm=newm;  void free_lvector(long *v, long nl, long nh)
          {
            free((FREE_ARG)(v+nl-NR_END));
       } /* end mult */  }
        
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  /******************* imatrix *******************************/
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       ipmx +=1;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       sw += weight[i];  { 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     } /* end of wave */    int **m; 
   } /* end of individual */    
     /* allocate pointers to rows */ 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    if (!m) nrerror("allocation failure 1 in matrix()"); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    m += NR_END; 
   return -l;    m -= nrl; 
 }    
     
     /* allocate rows and set pointers to them */ 
 /*********** Maximum Likelihood Estimation ***************/    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    m[nrl] += NR_END; 
 {    m[nrl] -= ncl; 
   int i,j, iter;    
   double **xi,*delti;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   double fret;    
   xi=matrix(1,npar,1,npar);    /* return pointer to array of pointers to rows */ 
   for (i=1;i<=npar;i++)    return m; 
     for (j=1;j<=npar;j++)  } 
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");  fprintf(ficlog,"Powell\n");  /****************** free_imatrix *************************/
   powell(p,xi,npar,ftol,&iter,&fret,func);  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        long nch,ncl,nrh,nrl; 
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));       /* free an int matrix allocated by imatrix() */ 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 }    free((FREE_ARG) (m+nrl-NR_END)); 
   } 
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /******************* matrix *******************************/
 {  double **matrix(long nrl, long nrh, long ncl, long nch)
   double  **a,**y,*x,pd;  {
   double **hess;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   int i, j,jk;    double **m;
   int *indx;  
     m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double hessii(double p[], double delta, int theta, double delti[]);    if (!m) nrerror("allocation failure 1 in matrix()");
   double hessij(double p[], double delti[], int i, int j);    m += NR_END;
   void lubksb(double **a, int npar, int *indx, double b[]) ;    m -= nrl;
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   hess=matrix(1,npar,1,npar);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
   printf("\nCalculation of the hessian matrix. Wait...\n");    m[nrl] -= ncl;
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     printf("%d",i);fflush(stdout);    return m;
     fprintf(ficlog,"%d",i);fflush(ficlog);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
     hess[i][i]=hessii(p,ftolhess,i,delti);  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
     /*printf(" %f ",p[i]);*/  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
     /*printf(" %lf ",hess[i][i]);*/     */
   }  }
    
   for (i=1;i<=npar;i++) {  /*************************free matrix ************************/
     for (j=1;j<=npar;j++)  {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       if (j>i) {  {
         printf(".%d%d",i,j);fflush(stdout);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);    free((FREE_ARG)(m+nrl-NR_END));
         hess[i][j]=hessij(p,delti,i,j);  }
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/  /******************* ma3x *******************************/
       }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     }  {
   }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   printf("\n");    double ***m;
   fprintf(ficlog,"\n");  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    if (!m) nrerror("allocation failure 1 in matrix()");
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    m += NR_END;
      m -= nrl;
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   x=vector(1,npar);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   indx=ivector(1,npar);    m[nrl] += NR_END;
   for (i=1;i<=npar;i++)    m[nrl] -= ncl;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  
   ludcmp(a,npar,indx,&pd);    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++) 
       matcov[i][j]=x[i];      m[nrl][j]=m[nrl][j-1]+nlay;
     }    
   }    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   printf("\n#Hessian matrix#\n");      for (j=ncl+1; j<=nch; j++) 
   fprintf(ficlog,"\n#Hessian matrix#\n");        m[i][j]=m[i][j-1]+nlay;
   for (i=1;i<=npar;i++) {    }
     for (j=1;j<=npar;j++) {    return m; 
       printf("%.3e ",hess[i][j]);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       fprintf(ficlog,"%.3e ",hess[i][j]);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     }    */
     printf("\n");  }
     fprintf(ficlog,"\n");  
   }  /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   /* Recompute Inverse */  {
   for (i=1;i<=npar;i++)    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   ludcmp(a,npar,indx,&pd);    free((FREE_ARG)(m+nrl-NR_END));
   }
   /*  printf("\n#Hessian matrix recomputed#\n");  
   /*************** function subdirf ***********/
   for (j=1;j<=npar;j++) {  char *subdirf(char fileres[])
     for (i=1;i<=npar;i++) x[i]=0;  {
     x[j]=1;    /* Caution optionfilefiname is hidden */
     lubksb(a,npar,indx,x);    strcpy(tmpout,optionfilefiname);
     for (i=1;i<=npar;i++){    strcat(tmpout,"/"); /* Add to the right */
       y[i][j]=x[i];    strcat(tmpout,fileres);
       printf("%.3e ",y[i][j]);    return tmpout;
       fprintf(ficlog,"%.3e ",y[i][j]);  }
     }  
     printf("\n");  /*************** function subdirf2 ***********/
     fprintf(ficlog,"\n");  char *subdirf2(char fileres[], char *preop)
   }  {
   */    
     /* Caution optionfilefiname is hidden */
   free_matrix(a,1,npar,1,npar);    strcpy(tmpout,optionfilefiname);
   free_matrix(y,1,npar,1,npar);    strcat(tmpout,"/");
   free_vector(x,1,npar);    strcat(tmpout,preop);
   free_ivector(indx,1,npar);    strcat(tmpout,fileres);
   free_matrix(hess,1,npar,1,npar);    return tmpout;
   }
   
 }  /*************** function subdirf3 ***********/
   char *subdirf3(char fileres[], char *preop, char *preop2)
 /*************** hessian matrix ****************/  {
 double hessii( double x[], double delta, int theta, double delti[])    
 {    /* Caution optionfilefiname is hidden */
   int i;    strcpy(tmpout,optionfilefiname);
   int l=1, lmax=20;    strcat(tmpout,"/");
   double k1,k2;    strcat(tmpout,preop);
   double p2[NPARMAX+1];    strcat(tmpout,preop2);
   double res;    strcat(tmpout,fileres);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    return tmpout;
   double fx;  }
   int k=0,kmax=10;  
   double l1;  /***************** f1dim *************************/
   extern int ncom; 
   fx=func(x);  extern double *pcom,*xicom;
   for (i=1;i<=npar;i++) p2[i]=x[i];  extern double (*nrfunc)(double []); 
   for(l=0 ; l <=lmax; l++){   
     l1=pow(10,l);  double f1dim(double x) 
     delts=delt;  { 
     for(k=1 ; k <kmax; k=k+1){    int j; 
       delt = delta*(l1*k);    double f;
       p2[theta]=x[theta] +delt;    double *xt; 
       k1=func(p2)-fx;   
       p2[theta]=x[theta]-delt;    xt=vector(1,ncom); 
       k2=func(p2)-fx;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    f=(*nrfunc)(xt); 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    free_vector(xt,1,ncom); 
          return f; 
 #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);  /*****************brent *************************/
 #endif  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  { 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    int iter; 
         k=kmax;    double a,b,d,etemp;
       }    double fu=0,fv,fw,fx;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    double ftemp;
         k=kmax; l=lmax*10.;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       }    double e=0.0; 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){   
         delts=delt;    a=(ax < cx ? ax : cx); 
       }    b=(ax > cx ? ax : cx); 
     }    x=w=v=bx; 
   }    fw=fv=fx=(*f)(x); 
   delti[theta]=delts;    for (iter=1;iter<=ITMAX;iter++) { 
   return res;      xm=0.5*(a+b); 
        tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
 double hessij( double x[], double delti[], int thetai,int thetaj)      fprintf(ficlog,".");fflush(ficlog);
 {  #ifdef DEBUG
   int i;      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);
   int l=1, l1, lmax=20;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   double k1,k2,k3,k4,res,fx;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   double p2[NPARMAX+1];  #endif
   int k;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
   fx=func(x);        return fx; 
   for (k=1; k<=2; k++) {      } 
     for (i=1;i<=npar;i++) p2[i]=x[i];      ftemp=fu;
     p2[thetai]=x[thetai]+delti[thetai]/k;      if (fabs(e) > tol1) { 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        r=(x-w)*(fx-fv); 
     k1=func(p2)-fx;        q=(x-v)*(fx-fw); 
          p=(x-v)*q-(x-w)*r; 
     p2[thetai]=x[thetai]+delti[thetai]/k;        q=2.0*(q-r); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        if (q > 0.0) p = -p; 
     k2=func(p2)-fx;        q=fabs(q); 
          etemp=e; 
     p2[thetai]=x[thetai]-delti[thetai]/k;        e=d; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     k3=func(p2)-fx;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
          else { 
     p2[thetai]=x[thetai]-delti[thetai]/k;          d=p/q; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          u=x+d; 
     k4=func(p2)-fx;          if (u-a < tol2 || b-u < tol2) 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */            d=SIGN(tol1,xm-x); 
 #ifdef DEBUG        } 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);      } else { 
     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);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 #endif      } 
   }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   return res;      fu=(*f)(u); 
 }      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
 /************** Inverse of matrix **************/        SHFT(v,w,x,u) 
 void ludcmp(double **a, int n, int *indx, double *d)          SHFT(fv,fw,fx,fu) 
 {          } else { 
   int i,imax,j,k;            if (u < x) a=u; else b=u; 
   double big,dum,sum,temp;            if (fu <= fw || w == x) { 
   double *vv;              v=w; 
                w=u; 
   vv=vector(1,n);              fv=fw; 
   *d=1.0;              fw=fu; 
   for (i=1;i<=n;i++) {            } else if (fu <= fv || v == x || v == w) { 
     big=0.0;              v=u; 
     for (j=1;j<=n;j++)              fv=fu; 
       if ((temp=fabs(a[i][j])) > big) big=temp;            } 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          } 
     vv[i]=1.0/big;    } 
   }    nrerror("Too many iterations in brent"); 
   for (j=1;j<=n;j++) {    *xmin=x; 
     for (i=1;i<j;i++) {    return fx; 
       sum=a[i][j];  } 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  /****************** mnbrak ***********************/
     }  
     big=0.0;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     for (i=j;i<=n;i++) {              double (*func)(double)) 
       sum=a[i][j];  { 
       for (k=1;k<j;k++)    double ulim,u,r,q, dum;
         sum -= a[i][k]*a[k][j];    double fu; 
       a[i][j]=sum;   
       if ( (dum=vv[i]*fabs(sum)) >= big) {    *fa=(*func)(*ax); 
         big=dum;    *fb=(*func)(*bx); 
         imax=i;    if (*fb > *fa) { 
       }      SHFT(dum,*ax,*bx,dum) 
     }        SHFT(dum,*fb,*fa,dum) 
     if (j != imax) {        } 
       for (k=1;k<=n;k++) {    *cx=(*bx)+GOLD*(*bx-*ax); 
         dum=a[imax][k];    *fc=(*func)(*cx); 
         a[imax][k]=a[j][k];    while (*fb > *fc) { 
         a[j][k]=dum;      r=(*bx-*ax)*(*fb-*fc); 
       }      q=(*bx-*cx)*(*fb-*fa); 
       *d = -(*d);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       vv[imax]=vv[j];        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     indx[j]=imax;      if ((*bx-u)*(u-*cx) > 0.0) { 
     if (a[j][j] == 0.0) a[j][j]=TINY;        fu=(*func)(u); 
     if (j != n) {      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       dum=1.0/(a[j][j]);        fu=(*func)(u); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        if (fu < *fc) { 
     }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   }            SHFT(*fb,*fc,fu,(*func)(u)) 
   free_vector(vv,1,n);  /* Doesn't work */            } 
 ;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 }        u=ulim; 
         fu=(*func)(u); 
 void lubksb(double **a, int n, int *indx, double b[])      } else { 
 {        u=(*cx)+GOLD*(*cx-*bx); 
   int i,ii=0,ip,j;        fu=(*func)(u); 
   double sum;      } 
        SHFT(*ax,*bx,*cx,u) 
   for (i=1;i<=n;i++) {        SHFT(*fa,*fb,*fc,fu) 
     ip=indx[i];        } 
     sum=b[ip];  } 
     b[ip]=b[i];  
     if (ii)  /*************** linmin ************************/
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;  int ncom; 
     b[i]=sum;  double *pcom,*xicom;
   }  double (*nrfunc)(double []); 
   for (i=n;i>=1;i--) {   
     sum=b[i];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  { 
     b[i]=sum/a[i][i];    double brent(double ax, double bx, double cx, 
   }                 double (*f)(double), double tol, double *xmin); 
 }    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 /************ Frequencies ********************/                double *fc, double (*func)(double)); 
 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)    int j; 
 {  /* Some frequencies */    double xx,xmin,bx,ax; 
      double fx,fb,fa;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;   
   int first;    ncom=n; 
   double ***freq; /* Frequencies */    pcom=vector(1,n); 
   double *pp;    xicom=vector(1,n); 
   double pos, k2, dateintsum=0,k2cpt=0;    nrfunc=func; 
   FILE *ficresp;    for (j=1;j<=n;j++) { 
   char fileresp[FILENAMELENGTH];      pcom[j]=p[j]; 
        xicom[j]=xi[j]; 
   pp=vector(1,nlstate);    } 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    ax=0.0; 
   strcpy(fileresp,"p");    xx=1.0; 
   strcat(fileresp,fileres);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   if((ficresp=fopen(fileresp,"w"))==NULL) {    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     printf("Problem with prevalence resultfile: %s\n", fileresp);  #ifdef DEBUG
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     exit(0);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   }  #endif
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    for (j=1;j<=n;j++) { 
   j1=0;      xi[j] *= xmin; 
        p[j] += xi[j]; 
   j=cptcoveff;    } 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
   first=1;  } 
   
   for(k1=1; k1<=j;k1++){  char *asc_diff_time(long time_sec, char ascdiff[])
     for(i1=1; i1<=ncodemax[k1];i1++){  {
       j1++;    long sec_left, days, hours, minutes;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    days = (time_sec) / (60*60*24);
         scanf("%d", i);*/    sec_left = (time_sec) % (60*60*24);
       for (i=-1; i<=nlstate+ndeath; i++)      hours = (sec_left) / (60*60) ;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      sec_left = (sec_left) %(60*60);
           for(m=agemin; m <= agemax+3; m++)    minutes = (sec_left) /60;
             freq[i][jk][m]=0;    sec_left = (sec_left) % (60);
          sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
       dateintsum=0;    return ascdiff;
       k2cpt=0;  }
       for (i=1; i<=imx; i++) {  
         bool=1;  /*************** powell ************************/
         if  (cptcovn>0) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
           for (z1=1; z1<=cptcoveff; z1++)              double (*func)(double [])) 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  { 
               bool=0;    void linmin(double p[], double xi[], int n, double *fret, 
         }                double (*func)(double [])); 
         if (bool==1) {    int i,ibig,j; 
           for(m=firstpass; m<=lastpass; m++){    double del,t,*pt,*ptt,*xit;
             k2=anint[m][i]+(mint[m][i]/12.);    double fp,fptt;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    double *xits;
               if(agev[m][i]==0) agev[m][i]=agemax+1;    int niterf, itmp;
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {    pt=vector(1,n); 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    ptt=vector(1,n); 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    xit=vector(1,n); 
               }    xits=vector(1,n); 
                  *fret=(*func)(p); 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    for (j=1;j<=n;j++) pt[j]=p[j]; 
                 dateintsum=dateintsum+k2;      rcurr_time = time(NULL);  
                 k2cpt++;    for (*iter=1;;++(*iter)) { 
               }      fp=(*fret); 
             }      ibig=0; 
           }      del=0.0; 
         }      rlast_time=rcurr_time;
       }      /* (void) gettimeofday(&curr_time,&tzp); */
              rcurr_time = time(NULL);  
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      curr_time = *localtime(&rcurr_time);
       printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       if  (cptcovn>0) {      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
         fprintf(ficresp, "\n#********** Variable ");  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);     for (i=1;i<=n;i++) {
         fprintf(ficresp, "**********\n#");        printf(" %d %.12f",i, p[i]);
       }        fprintf(ficlog," %d %.12lf",i, p[i]);
       for(i=1; i<=nlstate;i++)        fprintf(ficrespow," %.12lf", p[i]);
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      }
       fprintf(ficresp, "\n");      printf("\n");
            fprintf(ficlog,"\n");
       for(i=(int)agemin; i <= (int)agemax+3; i++){      fprintf(ficrespow,"\n");fflush(ficrespow);
         if(i==(int)agemax+3){      if(*iter <=3){
           fprintf(ficlog,"Total");        tml = *localtime(&rcurr_time);
         }else{        strcpy(strcurr,asctime(&tml));
           if(first==1){  /*       asctime_r(&tm,strcurr); */
             first=0;        rforecast_time=rcurr_time; 
             printf("See log file for details...\n");        itmp = strlen(strcurr);
           }        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           fprintf(ficlog,"Age %d", i);          strcurr[itmp-1]='\0';
         }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
         for(jk=1; jk <=nlstate ; jk++){        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for(niterf=10;niterf<=30;niterf+=10){
             pp[jk] += freq[jk][m][i];          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         }          forecast_time = *localtime(&rforecast_time);
         for(jk=1; jk <=nlstate ; jk++){  /*      asctime_r(&tmf,strfor); */
           for(m=-1, pos=0; m <=0 ; m++)          strcpy(strfor,asctime(&forecast_time));
             pos += freq[jk][m][i];          itmp = strlen(strfor);
           if(pp[jk]>=1.e-10){          if(strfor[itmp-1]=='\n')
             if(first==1){          strfor[itmp-1]='\0';
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
             }          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        }
           }else{      }
             if(first==1)      for (i=1;i<=n;i++) { 
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        fptt=(*fret); 
           }  #ifdef DEBUG
         }        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
         for(jk=1; jk <=nlstate ; jk++){  #endif
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        printf("%d",i);fflush(stdout);
             pp[jk] += freq[jk][m][i];        fprintf(ficlog,"%d",i);fflush(ficlog);
         }        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
         for(jk=1,pos=0; jk <=nlstate ; jk++)          del=fabs(fptt-(*fret)); 
           pos += pp[jk];          ibig=i; 
         for(jk=1; jk <=nlstate ; jk++){        } 
           if(pos>=1.e-5){  #ifdef DEBUG
             if(first==1)        printf("%d %.12e",i,(*fret));
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        fprintf(ficlog,"%d %.12e",i,(*fret));
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        for (j=1;j<=n;j++) {
           }else{          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
             if(first==1)          printf(" x(%d)=%.12e",j,xit[j]);
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        }
           }        for(j=1;j<=n;j++) {
           if( i <= (int) agemax){          printf(" p=%.12e",p[j]);
             if(pos>=1.e-5){          fprintf(ficlog," p=%.12e",p[j]);
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        }
               probs[i][jk][j1]= pp[jk]/pos;        printf("\n");
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        fprintf(ficlog,"\n");
             }  #endif
             else      } 
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
           }  #ifdef DEBUG
         }        int k[2],l;
                k[0]=1;
         for(jk=-1; jk <=nlstate+ndeath; jk++)        k[1]=-1;
           for(m=-1; m <=nlstate+ndeath; m++)        printf("Max: %.12e",(*func)(p));
             if(freq[jk][m][i] !=0 ) {        fprintf(ficlog,"Max: %.12e",(*func)(p));
             if(first==1)        for (j=1;j<=n;j++) {
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          printf(" %.12e",p[j]);
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);          fprintf(ficlog," %.12e",p[j]);
             }        }
         if(i <= (int) agemax)        printf("\n");
           fprintf(ficresp,"\n");        fprintf(ficlog,"\n");
         if(first==1)        for(l=0;l<=1;l++) {
           printf("Others in log...\n");          for (j=1;j<=n;j++) {
         fprintf(ficlog,"\n");            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       }            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]);
   }          }
   dateintmean=dateintsum/k2cpt;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
            fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   fclose(ficresp);        }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  #endif
   free_vector(pp,1,nlstate);  
    
   /* End of Freq */        free_vector(xit,1,n); 
 }        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
 /************ Prevalence ********************/        free_vector(pt,1,n); 
 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)        return; 
 {  /* Some frequencies */      } 
        if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      for (j=1;j<=n;j++) { 
   double ***freq; /* Frequencies */        ptt[j]=2.0*p[j]-pt[j]; 
   double *pp;        xit[j]=p[j]-pt[j]; 
   double pos, k2;        pt[j]=p[j]; 
       } 
   pp=vector(1,nlstate);      fptt=(*func)(ptt); 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (fptt < fp) { 
          t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        if (t < 0.0) { 
   j1=0;          linmin(p,xit,n,fret,func); 
            for (j=1;j<=n;j++) { 
   j=cptcoveff;            xi[j][ibig]=xi[j][n]; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            xi[j][n]=xit[j]; 
            }
   for(k1=1; k1<=j;k1++){  #ifdef DEBUG
     for(i1=1; i1<=ncodemax[k1];i1++){          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       j1++;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                for(j=1;j<=n;j++){
       for (i=-1; i<=nlstate+ndeath; i++)              printf(" %.12e",xit[j]);
         for (jk=-1; jk<=nlstate+ndeath; jk++)              fprintf(ficlog," %.12e",xit[j]);
           for(m=agemin; m <= agemax+3; m++)          }
             freq[i][jk][m]=0;          printf("\n");
                fprintf(ficlog,"\n");
       for (i=1; i<=imx; i++) {  #endif
         bool=1;        }
         if  (cptcovn>0) {      } 
           for (z1=1; z1<=cptcoveff; z1++)    } 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  } 
               bool=0;  
         }  /**** Prevalence limit (stable or period prevalence)  ****************/
         if (bool==1) {  
           for(m=firstpass; m<=lastpass; m++){  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
             k2=anint[m][i]+(mint[m][i]/12.);  {
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
               if(agev[m][i]==0) agev[m][i]=agemax+1;       matrix by transitions matrix until convergence is reached */
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               if (m<lastpass) {    int i, ii,j,k;
                 if (calagedate>0)    double min, max, maxmin, maxmax,sumnew=0.;
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    /* double **matprod2(); */ /* test */
                 else    double **out, cov[NCOVMAX+1], **pmij();
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double **newm;
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];    double agefin, delaymax=50 ; /* Max number of years to converge */
               }  
             }    for (ii=1;ii<=nlstate+ndeath;ii++)
           }      for (j=1;j<=nlstate+ndeath;j++){
         }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }      }
       for(i=(int)agemin; i <= (int)agemax+3; i++){  
         for(jk=1; jk <=nlstate ; jk++){     cov[1]=1.;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)   
             pp[jk] += freq[jk][m][i];   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         }    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
         for(jk=1; jk <=nlstate ; jk++){      newm=savm;
           for(m=-1, pos=0; m <=0 ; m++)      /* Covariates have to be included here again */
             pos += freq[jk][m][i];      cov[2]=agefin;
         }      
              for (k=1; k<=cptcovn;k++) {
         for(jk=1; jk <=nlstate ; jk++){        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        /*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]]);*/
             pp[jk] += freq[jk][m][i];      }
         }      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
              /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
              
         for(jk=1; jk <=nlstate ; jk++){          /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
           if( i <= (int) agemax){      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
             if(pos>=1.e-5){      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
               probs[i][jk][j1]= pp[jk]/pos;      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
             }      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
           }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
         }/* end jk */      
       }/* end i */      savm=oldm;
     } /* end i1 */      oldm=newm;
   } /* end k1 */      maxmax=0.;
       for(j=1;j<=nlstate;j++){
          min=1.;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        max=0.;
   free_vector(pp,1,nlstate);        for(i=1; i<=nlstate; i++) {
            sumnew=0;
 }  /* End of Freq */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           prlim[i][j]= newm[i][j]/(1-sumnew);
 /************* Waves Concatenation ***************/          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
           max=FMAX(max,prlim[i][j]);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          min=FMIN(min,prlim[i][j]);
 {        }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        maxmin=max-min;
      Death is a valid wave (if date is known).        maxmax=FMAX(maxmax,maxmin);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      }
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      if(maxmax < ftolpl){
      and mw[mi+1][i]. dh depends on stepm.        return prlim;
      */      }
     }
   int i, mi, m;  }
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  
      double sum=0., jmean=0.;*/  /*************** transition probabilities ***************/ 
   int first;  
   int j, k=0,jk, ju, jl;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   double sum=0.;  {
   first=0;    /* According to parameters values stored in x and the covariate's values stored in cov,
   jmin=1e+5;       computes the probability to be observed in state j being in state i by appying the
   jmax=-1;       model to the ncovmodel covariates (including constant and age).
   jmean=0.;       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
   for(i=1; i<=imx; i++){       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
     mi=0;       ncth covariate in the global vector x is given by the formula:
     m=firstpass;       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
     while(s[m][i] <= nlstate){       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
       if(s[m][i]>=1)       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
         mw[++mi][i]=m;       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
       if(m >=lastpass)       Outputs ps[i][j] the probability to be observed in j being in j according to
         break;       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
       else    */
         m++;    double s1, lnpijopii;
     }/* end while */    /*double t34;*/
     if (s[m][i] > nlstate){    int i,j,j1, nc, ii, jj;
       mi++;     /* Death is another wave */  
       /* if(mi==0)  never been interviewed correctly before death */      for(i=1; i<= nlstate; i++){
          /* Only death is a correct wave */        for(j=1; j<i;j++){
       mw[mi][i]=m;          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];
     wav[i]=mi;  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     if(mi==0){          }
       if(first==0){          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         first=1;        }
       }        for(j=i+1; j<=nlstate+ndeath;j++){
       if(first==1){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
       }            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
     } /* end mi==0 */  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
   }          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
   for(i=1; i<=imx; i++){        }
     for(mi=1; mi<wav[i];mi++){      }
       if (stepm <=0)      
         dh[mi][i]=1;      for(i=1; i<= nlstate; i++){
       else{        s1=0;
         if (s[mw[mi+1][i]][i] > nlstate) {        for(j=1; j<i; j++){
           if (agedc[i] < 2*AGESUP) {          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           if(j==0) j=1;  /* Survives at least one month after exam */        }
           k=k+1;        for(j=i+1; j<=nlstate+ndeath; j++){
           if (j >= jmax) jmax=j;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           if (j <= jmin) jmin=j;          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           sum=sum+j;        }
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
           }        ps[i][i]=1./(s1+1.);
         }        /* Computing other pijs */
         else{        for(j=1; j<i; j++)
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          ps[i][j]= exp(ps[i][j])*ps[i][i];
           k=k+1;        for(j=i+1; j<=nlstate+ndeath; j++)
           if (j >= jmax) jmax=j;          ps[i][j]= exp(ps[i][j])*ps[i][i];
           else if (j <= jmin)jmin=j;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      } /* end i */
           sum=sum+j;      
         }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         jk= j/stepm;        for(jj=1; jj<= nlstate+ndeath; jj++){
         jl= j -jk*stepm;          ps[ii][jj]=0;
         ju= j -(jk+1)*stepm;          ps[ii][ii]=1;
         if(jl <= -ju)        }
           dh[mi][i]=jk;      }
         else      
           dh[mi][i]=jk+1;      
         if(dh[mi][i]==0)      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
           dh[mi][i]=1; /* At least one step */      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
       }      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
     }      /*   } */
   }      /*   printf("\n "); */
   jmean=sum/k;      /* } */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      /* printf("\n ");printf("%lf ",cov[2]);*/
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      /*
  }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
         goto end;*/
 /*********** Tricode ****************************/      return ps;
 void tricode(int *Tvar, int **nbcode, int imx)  }
 {  
   int Ndum[20],ij=1, k, j, i;  /**************** Product of 2 matrices ******************/
   int cptcode=0;  
   cptcoveff=0;  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
    {
   for (k=0; k<19; k++) Ndum[k]=0;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   for (k=1; k<=7; k++) ncodemax[k]=0;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {       before: only the contents of out is modified. The function returns
     for (i=1; i<=imx; i++) {       a pointer to pointers identical to out */
       ij=(int)(covar[Tvar[j]][i]);    int i, j, k;
       Ndum[ij]++;    for(i=nrl; i<= nrh; i++)
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      for(k=ncolol; k<=ncoloh; k++){
       if (ij > cptcode) cptcode=ij;        out[i][k]=0.;
     }        for(j=ncl; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
     for (i=0; i<=cptcode; i++) {      }
       if(Ndum[i]!=0) ncodemax[j]++;    return out;
     }  }
     ij=1;  
   
   /************* Higher Matrix Product ***************/
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         if (Ndum[k] != 0) {  {
           nbcode[Tvar[j]][ij]=k;    /* Computes the transition matrix starting at age 'age' over 
                 'nhstepm*hstepm*stepm' months (i.e. until
           ij++;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         }       nhstepm*hstepm matrices. 
         if (ij > ncodemax[j]) break;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       }         (typically every 2 years instead of every month which is too big 
     }       for the memory).
   }         Model is determined by parameters x and covariates have to be 
        included manually here. 
  for (k=0; k<19; k++) Ndum[k]=0;  
        */
  for (i=1; i<=ncovmodel-2; i++) {  
    ij=Tvar[i];    int i, j, d, h, k;
    Ndum[ij]++;    double **out, cov[NCOVMAX+1];
  }    double **newm;
   
  ij=1;    /* Hstepm could be zero and should return the unit matrix */
  for (i=1; i<=10; i++) {    for (i=1;i<=nlstate+ndeath;i++)
    if((Ndum[i]!=0) && (i<=ncovcol)){      for (j=1;j<=nlstate+ndeath;j++){
      Tvaraff[ij]=i;        oldm[i][j]=(i==j ? 1.0 : 0.0);
      ij++;        po[i][j][0]=(i==j ? 1.0 : 0.0);
    }      }
  }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
      for(h=1; h <=nhstepm; h++){
  cptcoveff=ij-1;      for(d=1; d <=hstepm; d++){
 }        newm=savm;
         /* Covariates have to be included here again */
 /*********** Health Expectancies ****************/        cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )        for (k=1; k<=cptcovn;k++) 
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 {        for (k=1; k<=cptcovage;k++)
   /* Health expectancies */          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   double age, agelim, hf;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double ***p3mat,***varhe;  
   double **dnewm,**doldm;  
   double *xp;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   double **gp, **gm;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   double ***gradg, ***trgradg;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   int theta;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);        oldm=newm;
   xp=vector(1,npar);      }
   dnewm=matrix(1,nlstate*2,1,npar);      for(i=1; i<=nlstate+ndeath; i++)
   doldm=matrix(1,nlstate*2,1,nlstate*2);        for(j=1;j<=nlstate+ndeath;j++) {
            po[i][j][h]=newm[i][j];
   fprintf(ficreseij,"# Health expectancies\n");          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   fprintf(ficreseij,"# Age");        }
   for(i=1; i<=nlstate;i++)      /*printf("h=%d ",h);*/
     for(j=1; j<=nlstate;j++)    } /* end h */
       fprintf(ficreseij," %1d-%1d (SE)",i,j);  /*     printf("\n H=%d \n",h); */
   fprintf(ficreseij,"\n");    return po;
   }
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }  /*************** log-likelihood *************/
   else  hstepm=estepm;    double func( double *x)
   /* We compute the life expectancy from trapezoids spaced every estepm months  {
    * This is mainly to measure the difference between two models: for example    int i, ii, j, k, mi, d, kk;
    * if stepm=24 months pijx are given only every 2 years and by summing them    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    * we are calculating an estimate of the Life Expectancy assuming a linear    double **out;
    * progression inbetween and thus overestimating or underestimating according    double sw; /* Sum of weights */
    * to the curvature of the survival function. If, for the same date, we    double lli; /* Individual log likelihood */
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    int s1, s2;
    * to compare the new estimate of Life expectancy with the same linear    double bbh, survp;
    * hypothesis. A more precise result, taking into account a more precise    long ipmx;
    * curvature will be obtained if estepm is as small as stepm. */    /*extern weight */
     /* We are differentiating ll according to initial status */
   /* For example we decided to compute the life expectancy with the smallest unit */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    /*for(i=1;i<imx;i++) 
      nhstepm is the number of hstepm from age to agelim      printf(" %d\n",s[4][i]);
      nstepm is the number of stepm from age to agelin.    */
      Look at hpijx to understand the reason of that which relies in memory size    cov[1]=1.;
      and note for a fixed period like estepm months */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    for(k=1; k<=nlstate; k++) ll[k]=0.;
      survival function given by stepm (the optimization length). Unfortunately it  
      means that if the survival funtion is printed only each two years of age and if    if(mle==1){
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      results. So we changed our mind and took the option of the best precision.        /* 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[]
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
            to be observed in j being in i according to the model.
   agelim=AGESUP;         */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
     /* nhstepm age range expressed in number of stepm */          cov[2+k]=covar[Tvar[k]][i];
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        }
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
     /* if (stepm >= YEARM) hstepm=1;*/           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */           has been calculated etc */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(mi=1; mi<= wav[i]-1; mi++){
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          for (ii=1;ii<=nlstate+ndeath;ii++)
     gp=matrix(0,nhstepm,1,nlstate*2);            for (j=1;j<=nlstate+ndeath;j++){
     gm=matrix(0,nhstepm,1,nlstate*2);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          for(d=0; d<dh[mi][i]; d++){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
             }
     /* Computing Variances of health expectancies */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      for(theta=1; theta <=npar; theta++){            savm=oldm;
       for(i=1; i<=npar; i++){            oldm=newm;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          } /* end mult */
       }        
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
            /* But now since version 0.9 we anticipate for bias at large stepm.
       cptj=0;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       for(j=1; j<= nlstate; j++){           * (in months) between two waves is not a multiple of stepm, we rounded to 
         for(i=1; i<=nlstate; i++){           * the nearest (and in case of equal distance, to the lowest) interval but now
           cptj=cptj+1;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;           * probability in order to take into account the bias as a fraction of the way
           }           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         }           * -stepm/2 to stepm/2 .
       }           * For stepm=1 the results are the same as for previous versions of Imach.
                 * For stepm > 1 the results are less biased than in previous versions. 
                 */
       for(i=1; i<=npar; i++)          s1=s[mw[mi][i]][i];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          s2=s[mw[mi+1][i]][i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            bbh=(double)bh[mi][i]/(double)stepm; 
                /* bias bh is positive if real duration
       cptj=0;           * is higher than the multiple of stepm and negative otherwise.
       for(j=1; j<= nlstate; j++){           */
         for(i=1;i<=nlstate;i++){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           cptj=cptj+1;          if( s2 > nlstate){ 
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){            /* i.e. if s2 is a death state and if the date of death is known 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;               then the contribution to the likelihood is the probability to 
           }               die between last step unit time and current  step unit time, 
         }               which is also equal to probability to die before dh 
       }               minus probability to die before dh-stepm . 
       for(j=1; j<= nlstate*2; j++)               In version up to 0.92 likelihood was computed
         for(h=0; h<=nhstepm-1; h++){          as if date of death was unknown. Death was treated as any other
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          health state: the date of the interview describes the actual state
         }          and not the date of a change in health state. The former idea was
      }          to consider that at each interview the state was recorded
              (healthy, disable or death) and IMaCh was corrected; but when we
 /* End theta */          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);          contribution is smaller and very dependent of the step unit
           stepm. It is no more the probability to die between last interview
      for(h=0; h<=nhstepm-1; h++)          and month of death but the probability to survive from last
       for(j=1; j<=nlstate*2;j++)          interview up to one month before death multiplied by the
         for(theta=1; theta <=npar; theta++)          probability to die within a month. Thanks to Chris
           trgradg[h][j][theta]=gradg[h][theta][j];          Jackson for correcting this bug.  Former versions increased
                mortality artificially. The bad side is that we add another loop
           which slows down the processing. The difference can be up to 10%
      for(i=1;i<=nlstate*2;i++)          lower mortality.
       for(j=1;j<=nlstate*2;j++)            */
         varhe[i][j][(int)age] =0.;            lli=log(out[s1][s2] - savm[s1][s2]);
   
      printf("%d|",(int)age);fflush(stdout);  
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);          } else if  (s2==-2) {
      for(h=0;h<=nhstepm-1;h++){            for (j=1,survp=0. ; j<=nlstate; j++) 
       for(k=0;k<=nhstepm-1;k++){              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);            /*survp += out[s1][j]; */
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);            lli= log(survp);
         for(i=1;i<=nlstate*2;i++)          }
           for(j=1;j<=nlstate*2;j++)          
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          else if  (s2==-4) { 
       }            for (j=3,survp=0. ; j<=nlstate; j++)  
     }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     /* Computing expectancies */            lli= log(survp); 
     for(i=1; i<=nlstate;i++)          } 
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          else if  (s2==-5) { 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;            for (j=1,survp=0. ; j<=2; j++)  
                        survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/            lli= log(survp); 
           } 
         }          
           else{
     fprintf(ficreseij,"%3.0f",age );            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     cptj=0;            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
     for(i=1; i<=nlstate;i++)          } 
       for(j=1; j<=nlstate;j++){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         cptj++;          /*if(lli ==000.0)*/
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       }          ipmx +=1;
     fprintf(ficreseij,"\n");          sw += weight[i];
              ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     free_matrix(gm,0,nhstepm,1,nlstate*2);        } /* end of wave */
     free_matrix(gp,0,nhstepm,1,nlstate*2);      } /* end of individual */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    }  else if(mle==2){
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   printf("\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
   fprintf(ficlog,"\n");            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(xp,1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_matrix(dnewm,1,nlstate*2,1,npar);            }
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);          for(d=0; d<=dh[mi][i]; d++){
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);            newm=savm;
 }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
 /************ Variance ******************/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 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)            }
 {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* Variance of health expectancies */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            savm=oldm;
   /* double **newm;*/            oldm=newm;
   double **dnewm,**doldm;          } /* end mult */
   double **dnewmp,**doldmp;        
   int i, j, nhstepm, hstepm, h, nstepm ;          s1=s[mw[mi][i]][i];
   int k, cptcode;          s2=s[mw[mi+1][i]][i];
   double *xp;          bbh=(double)bh[mi][i]/(double)stepm; 
   double **gp, **gm;  /* for var eij */          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 */
   double ***gradg, ***trgradg; /*for var eij */          ipmx +=1;
   double **gradgp, **trgradgp; /* for var p point j */          sw += weight[i];
   double *gpp, *gmp; /* for var p point j */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */        } /* end of wave */
   double ***p3mat;      } /* end of individual */
   double age,agelim, hf;    }  else if(mle==3){  /* exponential inter-extrapolation */
   int theta;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   char digit[4];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   char digitp[16];        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   char fileresprobmorprev[FILENAMELENGTH];            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   if(popbased==1)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     strcpy(digitp,"-populbased-");            }
   else          for(d=0; d<dh[mi][i]; d++){
     strcpy(digitp,"-stablbased-");            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   strcpy(fileresprobmorprev,"prmorprev");            for (kk=1; kk<=cptcovage;kk++) {
   sprintf(digit,"%-d",ij);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/            }
   strcat(fileresprobmorprev,digit); /* Tvar to be done */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   strcat(fileresprobmorprev,digitp); /* Popbased or not */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   strcat(fileresprobmorprev,fileres);            savm=oldm;
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {            oldm=newm;
     printf("Problem with resultfile: %s\n", fileresprobmorprev);          } /* end mult */
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);        
   }          s1=s[mw[mi][i]][i];
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);          s2=s[mw[mi+1][i]][i];
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);          bbh=(double)bh[mi][i]/(double)stepm; 
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");          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 */
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);          ipmx +=1;
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){          sw += weight[i];
     fprintf(ficresprobmorprev," p.%-d SE",j);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(i=1; i<=nlstate;i++)        } /* end of wave */
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);      } /* end of individual */
   }      }else if (mle==4){  /* ml=4 no inter-extrapolation */
   fprintf(ficresprobmorprev,"\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);        for(mi=1; mi<= wav[i]-1; mi++){
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);          for (ii=1;ii<=nlstate+ndeath;ii++)
     exit(0);            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   else{              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficgp,"\n# Routine varevsij");            }
   }          for(d=0; d<dh[mi][i]; d++){
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {            newm=savm;
     printf("Problem with html file: %s\n", optionfilehtm);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);            for (kk=1; kk<=cptcovage;kk++) {
     exit(0);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
   else{          
     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");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);            savm=oldm;
             oldm=newm;
   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");          } /* end mult */
   fprintf(ficresvij,"# Age");        
   for(i=1; i<=nlstate;i++)          s1=s[mw[mi][i]][i];
     for(j=1; j<=nlstate;j++)          s2=s[mw[mi+1][i]][i];
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          if( s2 > nlstate){ 
   fprintf(ficresvij,"\n");            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
   xp=vector(1,npar);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   dnewm=matrix(1,nlstate,1,npar);          }
   doldm=matrix(1,nlstate,1,nlstate);          ipmx +=1;
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);          sw += weight[i];
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);        } /* end of wave */
   gpp=vector(nlstate+1,nlstate+ndeath);      } /* end of individual */
   gmp=vector(nlstate+1,nlstate+ndeath);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   if(estepm < stepm){        for(mi=1; mi<= wav[i]-1; mi++){
     printf ("Problem %d lower than %d\n",estepm, stepm);          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   else  hstepm=estepm;                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* For example we decided to compute the life expectancy with the smallest unit */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* 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          for(d=0; d<dh[mi][i]; d++){
      nstepm is the number of stepm from age to agelin.            newm=savm;
      Look at hpijx to understand the reason of that which relies in memory size            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      and note for a fixed period like k years */            for (kk=1; kk<=cptcovage;kk++) {
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      survival function given by stepm (the optimization length). Unfortunately it            }
      means that if the survival funtion is printed only each two years of age and if          
      you sum them up and add 1 year (area under the trapezoids) you won't get the same            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      results. So we changed our mind and took the option of the best precision.                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   */            savm=oldm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            oldm=newm;
   agelim = AGESUP;          } /* end mult */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          s1=s[mw[mi][i]][i];
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          s2=s[mw[mi+1][i]][i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          ipmx +=1;
     gp=matrix(0,nhstepm,1,nlstate);          sw += weight[i];
     gm=matrix(0,nhstepm,1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         } /* end of wave */
     for(theta=1; theta <=npar; theta++){      } /* end of individual */
       for(i=1; i<=npar; i++){ /* Computes gradient */    } /* End of if */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    return -l;
   }
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)  /*************** log-likelihood *************/
           prlim[i][i]=probs[(int)age][i][ij];  double funcone( double *x)
       }  {
      /* Same as likeli but slower because of a lot of printf and if */
       for(j=1; j<= nlstate; j++){    int i, ii, j, k, mi, d, kk;
         for(h=0; h<=nhstepm; h++){    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    double **out;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    double lli; /* Individual log likelihood */
         }    double llt;
       }    int s1, s2;
       /* This for computing forces of mortality (h=1)as a weighted average */    double bbh, survp;
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){    /*extern weight */
         for(i=1; i<= nlstate; i++)    /* We are differentiating ll according to initial status */
           gpp[j] += prlim[i][i]*p3mat[i][j][1];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       }        /*for(i=1;i<imx;i++) 
       /* end force of mortality */      printf(" %d\n",s[4][i]);
     */
       for(i=1; i<=npar; i++) /* Computes gradient */    cov[1]=1.;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      for(k=1; k<=nlstate; k++) ll[k]=0.;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
      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++)          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
           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 */          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
           /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
       for(j=1; j<= nlstate; j++) /* vareij */          savm=oldm;
         for(h=0; h<=nhstepm; h++){          oldm=newm;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        } /* end mult */
         }        
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */        s1=s[mw[mi][i]][i];
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];        s2=s[mw[mi+1][i]][i];
       }        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
     } /* End theta */         * is higher than the multiple of stepm and negative otherwise.
          */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
     for(h=0; h<=nhstepm; h++) /* veij */        } else if  (s2==-2) {
       for(j=1; j<=nlstate;j++)          for (j=1,survp=0. ; j<=nlstate; j++) 
         for(theta=1; theta <=npar; theta++)            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           trgradg[h][j][theta]=gradg[h][theta][j];          lli= log(survp);
         }else if (mle==1){
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for(theta=1; theta <=npar; theta++)        } else if(mle==2){
         trgradgp[j][theta]=gradgp[theta][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 */
         } else if(mle==3){  /* exponential inter-extrapolation */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     for(i=1;i<=nlstate;i++)        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       for(j=1;j<=nlstate;j++)          lli=log(out[s1][s2]); /* Original formula */
         vareij[i][j][(int)age] =0.;        } else{  /* mle=0 back to 1 */
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     for(h=0;h<=nhstepm;h++){          /*lli=log(out[s1][s2]); */ /* Original formula */
       for(k=0;k<=nhstepm;k++){        } /* End of if */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        ipmx +=1;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        sw += weight[i];
         for(i=1;i<=nlstate;i++)        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for(j=1;j<=nlstate;j++)        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        if(globpr){
       }          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
     }   %11.6f %11.6f %11.6f ", \
                   num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     /* pptj */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);            llt +=ll[k]*gipmx/gsw;
     for(j=nlstate+1;j<=nlstate+ndeath;j++)            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
       for(i=nlstate+1;i<=nlstate+ndeath;i++)          }
         varppt[j][i]=doldmp[j][i];          fprintf(ficresilk," %10.6f\n", -llt);
     /* end ppptj */        }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);        } /* end of wave */
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);    } /* end of individual */
      for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     if (popbased==1) {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for(i=1; i<=nlstate;i++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         prlim[i][i]=probs[(int)age][i][ij];    if(globpr==0){ /* First time we count the contributions and weights */
     }      gipmx=ipmx;
          gsw=sw;
     /* This for computing force of mortality (h=1)as a weighted average */    }
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){    return -l;
       for(i=1; i<= nlstate; i++)  }
         gmp[j] += prlim[i][i]*p3mat[i][j][1];  
     }      
     /* end force of mortality */  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);  {
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){    /* This routine should help understanding what is done with 
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));       the selection of individuals/waves and
       for(i=1; i<=nlstate;i++){       to check the exact contribution to the likelihood.
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);       Plotting could be done.
       }     */
     }    int k;
     fprintf(ficresprobmorprev,"\n");  
     if(*globpri !=0){ /* Just counts and sums, no printings */
     fprintf(ficresvij,"%.0f ",age );      strcpy(fileresilk,"ilk"); 
     for(i=1; i<=nlstate;i++)      strcat(fileresilk,fileres);
       for(j=1; j<=nlstate;j++){      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);        printf("Problem with resultfile: %s\n", fileresilk);
       }        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     fprintf(ficresvij,"\n");      }
     free_matrix(gp,0,nhstepm,1,nlstate);      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");
     free_matrix(gm,0,nhstepm,1,nlstate);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      for(k=1; k<=nlstate; k++) 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   } /* End age */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   free_vector(gpp,nlstate+1,nlstate+ndeath);    }
   free_vector(gmp,nlstate+1,nlstate+ndeath);  
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);    *fretone=(*funcone)(p);
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    if(*globpri !=0){
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");      fclose(ficresilk);
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");      fflush(fichtm); 
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);    } 
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);    return;
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);  }
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);  
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);  
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);  /*********** Maximum Likelihood Estimation ***************/
   
   free_vector(xp,1,npar);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   free_matrix(doldm,1,nlstate,1,nlstate);  {
   free_matrix(dnewm,1,nlstate,1,npar);    int i,j, iter;
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    double **xi;
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);    double fret;
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    double fretone; /* Only one call to likelihood */
   fclose(ficresprobmorprev);    /*  char filerespow[FILENAMELENGTH];*/
   fclose(ficgp);    xi=matrix(1,npar,1,npar);
   fclose(fichtm);    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
 }        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
 /************ Variance of prevlim ******************/    strcpy(filerespow,"pow"); 
 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)    strcat(filerespow,fileres);
 {    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   /* Variance of prevalence limit */      printf("Problem with resultfile: %s\n", filerespow);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   double **newm;    }
   double **dnewm,**doldm;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   int i, j, nhstepm, hstepm;    for (i=1;i<=nlstate;i++)
   int k, cptcode;      for(j=1;j<=nlstate+ndeath;j++)
   double *xp;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   double *gp, *gm;    fprintf(ficrespow,"\n");
   double **gradg, **trgradg;  
   double age,agelim;    powell(p,xi,npar,ftol,&iter,&fret,func);
   int theta;  
        free_matrix(xi,1,npar,1,npar);
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    fclose(ficrespow);
   fprintf(ficresvpl,"# Age");    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   for(i=1; i<=nlstate;i++)    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       fprintf(ficresvpl," %1d-%1d",i,i);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   fprintf(ficresvpl,"\n");  
   }
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);  /**** Computes Hessian and covariance matrix ***/
   doldm=matrix(1,nlstate,1,nlstate);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
    {
   hstepm=1*YEARM; /* Every year of age */    double  **a,**y,*x,pd;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double **hess;
   agelim = AGESUP;    int i, j,jk;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int *indx;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     if (stepm >= YEARM) hstepm=1;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     gradg=matrix(1,npar,1,nlstate);    void lubksb(double **a, int npar, int *indx, double b[]) ;
     gp=vector(1,nlstate);    void ludcmp(double **a, int npar, int *indx, double *d) ;
     gm=vector(1,nlstate);    double gompertz(double p[]);
     hess=matrix(1,npar,1,npar);
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */    printf("\nCalculation of the hessian matrix. Wait...\n");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       }    for (i=1;i<=npar;i++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      printf("%d",i);fflush(stdout);
       for(i=1;i<=nlstate;i++)      fprintf(ficlog,"%d",i);fflush(ficlog);
         gp[i] = prlim[i][i];     
           hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       for(i=1; i<=npar; i++) /* Computes gradient */      
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      /*  printf(" %f ",p[i]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       for(i=1;i<=nlstate;i++)    }
         gm[i] = prlim[i][i];    
     for (i=1;i<=npar;i++) {
       for(i=1;i<=nlstate;i++)      for (j=1;j<=npar;j++)  {
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        if (j>i) { 
     } /* End theta */          printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     trgradg =matrix(1,nlstate,1,npar);          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
     for(j=1; j<=nlstate;j++)          hess[j][i]=hess[i][j];    
       for(theta=1; theta <=npar; theta++)          /*printf(" %lf ",hess[i][j]);*/
         trgradg[j][theta]=gradg[theta][j];        }
       }
     for(i=1;i<=nlstate;i++)    }
       varpl[i][(int)age] =0.;    printf("\n");
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    fprintf(ficlog,"\n");
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  
     for(i=1;i<=nlstate;i++)    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
     fprintf(ficresvpl,"%.0f ",age );    a=matrix(1,npar,1,npar);
     for(i=1; i<=nlstate;i++)    y=matrix(1,npar,1,npar);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    x=vector(1,npar);
     fprintf(ficresvpl,"\n");    indx=ivector(1,npar);
     free_vector(gp,1,nlstate);    for (i=1;i<=npar;i++)
     free_vector(gm,1,nlstate);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     free_matrix(gradg,1,npar,1,nlstate);    ludcmp(a,npar,indx,&pd);
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
   free_vector(xp,1,npar);      x[j]=1;
   free_matrix(doldm,1,nlstate,1,npar);      lubksb(a,npar,indx,x);
   free_matrix(dnewm,1,nlstate,1,nlstate);      for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
 }      }
     }
 /************ Variance of one-step probabilities  ******************/  
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    printf("\n#Hessian matrix#\n");
 {    fprintf(ficlog,"\n#Hessian matrix#\n");
   int i, j=0,  i1, k1, l1, t, tj;    for (i=1;i<=npar;i++) { 
   int k2, l2, j1,  z1;      for (j=1;j<=npar;j++) { 
   int k=0,l, cptcode;        printf("%.3e ",hess[i][j]);
   int first=1, first1;        fprintf(ficlog,"%.3e ",hess[i][j]);
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;      }
   double **dnewm,**doldm;      printf("\n");
   double *xp;      fprintf(ficlog,"\n");
   double *gp, *gm;    }
   double **gradg, **trgradg;  
   double **mu;    /* Recompute Inverse */
   double age,agelim, cov[NCOVMAX];    for (i=1;i<=npar;i++)
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   int theta;    ludcmp(a,npar,indx,&pd);
   char fileresprob[FILENAMELENGTH];  
   char fileresprobcov[FILENAMELENGTH];    /*  printf("\n#Hessian matrix recomputed#\n");
   char fileresprobcor[FILENAMELENGTH];  
     for (j=1;j<=npar;j++) {
   double ***varpij;      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
   strcpy(fileresprob,"prob");      lubksb(a,npar,indx,x);
   strcat(fileresprob,fileres);      for (i=1;i<=npar;i++){ 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        y[i][j]=x[i];
     printf("Problem with resultfile: %s\n", fileresprob);        printf("%.3e ",y[i][j]);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);        fprintf(ficlog,"%.3e ",y[i][j]);
   }      }
   strcpy(fileresprobcov,"probcov");      printf("\n");
   strcat(fileresprobcov,fileres);      fprintf(ficlog,"\n");
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    }
     printf("Problem with resultfile: %s\n", fileresprobcov);    */
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);  
   }    free_matrix(a,1,npar,1,npar);
   strcpy(fileresprobcor,"probcor");    free_matrix(y,1,npar,1,npar);
   strcat(fileresprobcor,fileres);    free_vector(x,1,npar);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    free_ivector(indx,1,npar);
     printf("Problem with resultfile: %s\n", fileresprobcor);    free_matrix(hess,1,npar,1,npar);
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);  
   }  
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);  }
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);  
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);  /*************** hessian matrix ****************/
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);  {
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    int i;
      int l=1, lmax=20;
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    double k1,k2;
   fprintf(ficresprob,"# Age");    double p2[MAXPARM+1]; /* identical to x */
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    double res;
   fprintf(ficresprobcov,"# Age");    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    double fx;
   fprintf(ficresprobcov,"# Age");    int k=0,kmax=10;
     double l1;
   
   for(i=1; i<=nlstate;i++)    fx=func(x);
     for(j=1; j<=(nlstate+ndeath);j++){    for (i=1;i<=npar;i++) p2[i]=x[i];
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
       fprintf(ficresprobcov," p%1d-%1d ",i,j);      l1=pow(10,l);
       fprintf(ficresprobcor," p%1d-%1d ",i,j);      delts=delt;
     }        for(k=1 ; k <kmax; k=k+1){
   fprintf(ficresprob,"\n");        delt = delta*(l1*k);
   fprintf(ficresprobcov,"\n");        p2[theta]=x[theta] +delt;
   fprintf(ficresprobcor,"\n");        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
   xp=vector(1,npar);        p2[theta]=x[theta]-delt;
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);        k2=func(p2)-fx;
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));        /*res= (k1-2.0*fx+k2)/delt/delt; */
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);        
   first=1;  #ifdef DEBUGHESS
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        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);
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);  #endif
     exit(0);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   else{          k=kmax;
     fprintf(ficgp,"\n# Routine varprob");        }
   }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {          k=kmax; l=lmax*10.;
     printf("Problem with html file: %s\n", optionfilehtm);        }
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     exit(0);          delts=delt;
   }        }
   else{      }
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");    }
     fprintf(fichtm,"\n");    delti[theta]=delts;
     return res; 
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\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");  }
     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");  
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   }  {
     int i;
      int l=1, l1, lmax=20;
   cov[1]=1;    double k1,k2,k3,k4,res,fx;
   tj=cptcoveff;    double p2[MAXPARM+1];
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}    int k;
   j1=0;  
   for(t=1; t<=tj;t++){    fx=func(x);
     for(i1=1; i1<=ncodemax[t];i1++){    for (k=1; k<=2; k++) {
       j1++;      for (i=1;i<=npar;i++) p2[i]=x[i];
            p2[thetai]=x[thetai]+delti[thetai]/k;
       if  (cptcovn>0) {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         fprintf(ficresprob, "\n#********** Variable ");      k1=func(p2)-fx;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    
         fprintf(ficresprob, "**********\n#");      p2[thetai]=x[thetai]+delti[thetai]/k;
         fprintf(ficresprobcov, "\n#********** Variable ");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      k2=func(p2)-fx;
         fprintf(ficresprobcov, "**********\n#");    
              p2[thetai]=x[thetai]-delti[thetai]/k;
         fprintf(ficgp, "\n#********** Variable ");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      k3=func(p2)-fx;
         fprintf(ficgp, "**********\n#");    
              p2[thetai]=x[thetai]-delti[thetai]/k;
              p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");      k4=func(p2)-fx;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");  #ifdef DEBUG
              printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         fprintf(ficresprobcor, "\n#********** Variable ");          fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  #endif
         fprintf(ficgp, "**********\n#");        }
       }    return res;
        }
       for (age=bage; age<=fage; age ++){  
         cov[2]=age;  /************** Inverse of matrix **************/
         for (k=1; k<=cptcovn;k++) {  void ludcmp(double **a, int n, int *indx, double *d) 
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];  { 
         }    int i,imax,j,k; 
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    double big,dum,sum,temp; 
         for (k=1; k<=cptcovprod;k++)    double *vv; 
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];   
            vv=vector(1,n); 
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));    *d=1.0; 
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);    for (i=1;i<=n;i++) { 
         gp=vector(1,(nlstate)*(nlstate+ndeath));      big=0.0; 
         gm=vector(1,(nlstate)*(nlstate+ndeath));      for (j=1;j<=n;j++) 
            if ((temp=fabs(a[i][j])) > big) big=temp; 
         for(theta=1; theta <=npar; theta++){      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           for(i=1; i<=npar; i++)      vv[i]=1.0/big; 
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    } 
              for (j=1;j<=n;j++) { 
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      for (i=1;i<j;i++) { 
                  sum=a[i][j]; 
           k=0;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           for(i=1; i<= (nlstate); i++){        a[i][j]=sum; 
             for(j=1; j<=(nlstate+ndeath);j++){      } 
               k=k+1;      big=0.0; 
               gp[k]=pmmij[i][j];      for (i=j;i<=n;i++) { 
             }        sum=a[i][j]; 
           }        for (k=1;k<j;k++) 
                    sum -= a[i][k]*a[k][j]; 
           for(i=1; i<=npar; i++)        a[i][j]=sum; 
             xp[i] = x[i] - (i==theta ?delti[theta]:0);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
              big=dum; 
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          imax=i; 
           k=0;        } 
           for(i=1; i<=(nlstate); i++){      } 
             for(j=1; j<=(nlstate+ndeath);j++){      if (j != imax) { 
               k=k+1;        for (k=1;k<=n;k++) { 
               gm[k]=pmmij[i][j];          dum=a[imax][k]; 
             }          a[imax][k]=a[j][k]; 
           }          a[j][k]=dum; 
              } 
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)        *d = -(*d); 
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          vv[imax]=vv[j]; 
         }      } 
       indx[j]=imax; 
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)      if (a[j][j] == 0.0) a[j][j]=TINY; 
           for(theta=1; theta <=npar; theta++)      if (j != n) { 
             trgradg[j][theta]=gradg[theta][j];        dum=1.0/(a[j][j]); 
                for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         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);    } 
            free_vector(vv,1,n);  /* Doesn't work */
         pmij(pmmij,cov,ncovmodel,x,nlstate);  ;
          } 
         k=0;  
         for(i=1; i<=(nlstate); i++){  void lubksb(double **a, int n, int *indx, double b[]) 
           for(j=1; j<=(nlstate+ndeath);j++){  { 
             k=k+1;    int i,ii=0,ip,j; 
             mu[k][(int) age]=pmmij[i][j];    double sum; 
           }   
         }    for (i=1;i<=n;i++) { 
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)      ip=indx[i]; 
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)      sum=b[ip]; 
             varpij[i][j][(int)age] = doldm[i][j];      b[ip]=b[i]; 
       if (ii) 
         /*printf("\n%d ",(int)age);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){      else if (sum) ii=i; 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      b[i]=sum; 
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    } 
      }*/    for (i=n;i>=1;i--) { 
       sum=b[i]; 
         fprintf(ficresprob,"\n%d ",(int)age);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         fprintf(ficresprobcov,"\n%d ",(int)age);      b[i]=sum/a[i][i]; 
         fprintf(ficresprobcor,"\n%d ",(int)age);    } 
   } 
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)  
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));  void pstamp(FILE *fichier)
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  {
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);  }
         }  
         i=0;  /************ Frequencies ********************/
         for (k=1; k<=(nlstate);k++){  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
           for (l=1; l<=(nlstate+ndeath);l++){  {  /* Some frequencies */
             i=i++;    
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    int i, m, jk, k1,i1, j1, bool, z1,j;
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    int first;
             for (j=1; j<=i;j++){    double ***freq; /* Frequencies */
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);    double *pp, **prop;
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));    double pos,posprop, k2, dateintsum=0,k2cpt=0;
             }    char fileresp[FILENAMELENGTH];
           }    
         }/* end of loop for state */    pp=vector(1,nlstate);
       } /* end of loop for age */    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
       /* Confidence intervalle of pij  */    strcat(fileresp,fileres);
       /*    if((ficresp=fopen(fileresp,"w"))==NULL) {
       fprintf(ficgp,"\nset noparametric;unset label");      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");      exit(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);    }
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);    j1=0;
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);    
       */    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/  
       first1=1;    first=1;
       for (k1=1; k1<=(nlstate);k1++){  
         for (l1=1; l1<=(nlstate+ndeath);l1++){    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
           if(l1==k1) continue;    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
           i=(k1-1)*(nlstate+ndeath)+l1;    /*    j1++;
           for (k2=1; k2<=(nlstate);k2++){  */
             for (l2=1; l2<=(nlstate+ndeath);l2++){    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
               if(l2==k2) continue;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
               j=(k2-1)*(nlstate+ndeath)+l2;          scanf("%d", i);*/
               if(j<=i) continue;        for (i=-5; i<=nlstate+ndeath; i++)  
               for (age=bage; age<=fage; age ++){          for (jk=-5; jk<=nlstate+ndeath; jk++)  
                 if ((int)age %5==0){            for(m=iagemin; m <= iagemax+3; m++)
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;              freq[i][jk][m]=0;
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;        
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;        for (i=1; i<=nlstate; i++)  
                   mu1=mu[i][(int) age]/stepm*YEARM ;          for(m=iagemin; m <= iagemax+3; m++)
                   mu2=mu[j][(int) age]/stepm*YEARM;            prop[i][m]=0;
                   /* Computing eigen value of matrix of covariance */        
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));        dateintsum=0;
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));        k2cpt=0;
                   if(first1==1){        for (i=1; i<=imx; i++) {
                     first1=0;          bool=1;
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                   }            for (z1=1; z1<=cptcoveff; z1++)       
                   fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
                   /* Eigen vectors */                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));                bool=0;
                   v21=sqrt(1.-v11*v11);                /* 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", 
                   v12=-v21;                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
                   v22=v11;                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
                   /*printf(fignu*/                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */              } 
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */          }
                   if(first==1){   
                     first=0;          if (bool==1){
                     fprintf(ficgp,"\nset parametric;set nolabel");            for(m=firstpass; m<=lastpass; m++){
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);              k2=anint[m][i]+(mint[m][i]/12.);
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);                if (m<lastpass) {
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                     /*              fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \                }
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);                
                     */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                     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",\                  dateintsum=dateintsum+k2;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \                  k2cpt++;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));                }
                   }else{                /*}*/
                     first=0;            }
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);          }
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);        } /* end i */
                     /*         
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \        pstamp(ficresp);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);        if  (cptcovn>0) {
                     */          fprintf(ficresp, "\n#********** Variable "); 
                     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",\          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \          fprintf(ficresp, "**********\n#");
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));          fprintf(ficlog, "\n#********** Variable "); 
                   }/* if first */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                 } /* age mod 5 */          fprintf(ficlog, "**********\n#");
               } /* end loop age */        }
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);        for(i=1; i<=nlstate;i++) 
               first=1;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
             } /*l12 */        fprintf(ficresp, "\n");
           } /* k12 */        
         } /*l1 */        for(i=iagemin; i <= iagemax+3; i++){
       }/* k1 */          if(i==iagemax+3){
     } /* loop covariates */            fprintf(ficlog,"Total");
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);          }else{
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));            if(first==1){
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));              first=0;
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);              printf("See log file for details...\n");
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            }
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            fprintf(ficlog,"Age %d", i);
   }          }
   free_vector(xp,1,npar);          for(jk=1; jk <=nlstate ; jk++){
   fclose(ficresprob);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   fclose(ficresprobcov);              pp[jk] += freq[jk][m][i]; 
   fclose(ficresprobcor);          }
   fclose(ficgp);          for(jk=1; jk <=nlstate ; jk++){
   fclose(fichtm);            for(m=-1, pos=0; m <=0 ; m++)
 }              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
               if(first==1){
 /******************* Printing html file ***********/                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \              }
                   int lastpass, int stepm, int weightopt, char model[],\              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\            }else{
                   int popforecast, int estepm ,\              if(first==1)
                   double jprev1, double mprev1,double anprev1, \                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                   double jprev2, double mprev2,double anprev2){              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   int jj1, k1, i1, cpt;            }
   /*char optionfilehtm[FILENAMELENGTH];*/          }
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);          for(jk=1; jk <=nlstate ; jk++){
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   }              pp[jk] += freq[jk][m][i];
           }       
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
  - 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            pos += pp[jk];
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n            posprop += prop[jk][i];
  - 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):          for(jk=1; jk <=nlstate ; jk++){
    <a href=\"e%s\">e%s</a> <br>\n</li>", \            if(pos>=1.e-5){
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
  m=cptcoveff;              if(first==1)
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
  jj1=0;            }
  for(k1=1; k1<=m;k1++){            if( i <= iagemax){
    for(i1=1; i1<=ncodemax[k1];i1++){              if(pos>=1.e-5){
      jj1++;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
      if (cptcovn > 0) {                /*probs[i][jk][j1]= pp[jk]/pos;*/
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");                /*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 (cpt=1; cpt<=cptcoveff;cpt++)              }
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);              else
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
      }            }
      /* Pij */          }
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>          
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              for(jk=-1; jk <=nlstate+ndeath; jk++)
      /* Quasi-incidences */            for(m=-1; m <=nlstate+ndeath; m++)
      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>              if(freq[jk][m][i] !=0 ) {
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              if(first==1)
        /* Stable prevalence in each health state */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
        for(cpt=1; cpt<nlstate;cpt++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>              }
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          if(i <= iagemax)
        }            fprintf(ficresp,"\n");
      for(cpt=1; cpt<=nlstate;cpt++) {          if(first==1)
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>            printf("Others in log...\n");
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          fprintf(ficlog,"\n");
      }        }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        /*}*/
 health expectancies in states (1) and (2): e%s%d.png<br>    }
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    dateintmean=dateintsum/k2cpt; 
    } /* end i1 */   
  }/* End k1 */    fclose(ficresp);
  fprintf(fichtm,"</ul>");    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n    /* End of Freq */
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n  }
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n  
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n  /************ Prevalence ********************/
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n  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)
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n  {  
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
  - 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);       in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
  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    int i, m, jk, k1, i1, j1, bool, z1,j;
         <br>",fileres,fileres,fileres,fileres);    double ***freq; /* Frequencies */
  else    double *pp, **prop;
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);    double pos,posprop; 
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");    double  y2; /* in fractional years */
     int iagemin, iagemax;
  m=cptcoveff;    int first; /** to stop verbosity which is redirected to log file */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
     iagemin= (int) agemin;
  jj1=0;    iagemax= (int) agemax;
  for(k1=1; k1<=m;k1++){    /*pp=vector(1,nlstate);*/
    for(i1=1; i1<=ncodemax[k1];i1++){    prop=matrix(1,nlstate,iagemin,iagemax+3); 
      jj1++;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
      if (cptcovn > 0) {    j1=0;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    
        for (cpt=1; cpt<=cptcoveff;cpt++)    /*j=cptcoveff;*/
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    
      }    first=1;
      for(cpt=1; cpt<=nlstate;cpt++) {    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      /*for(i1=1; i1<=ncodemax[k1];i1++){
 interval) in state (%d): v%s%d%d.png <br>        j1++;*/
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          
      }        for (i=1; i<=nlstate; i++)  
    } /* end i1 */          for(m=iagemin; m <= iagemax+3; m++)
  }/* End k1 */            prop[i][m]=0.0;
  fprintf(fichtm,"</ul>");       
 fclose(fichtm);        for (i=1; i<=imx; i++) { /* Each individual */
 }          bool=1;
           if  (cptcovn>0) {
 /******************* Gnuplot file **************/            for (z1=1; z1<=cptcoveff; z1++) 
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          } 
   int ng;          if (bool==1) { 
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     printf("Problem with file %s",optionfilegnuplot);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
 #ifdef windows                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,"cd \"%s\" \n",pathc);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
 #endif                  /*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]]);*/
 m=pow(2,cptcoveff);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                    prop[s[m][i]][iagemax+3] += weight[i]; 
  /* 1eme*/                } 
   for (cpt=1; cpt<= nlstate ; cpt ++) {              }
    for (k1=1; k1<= m ; k1 ++) {            } /* end selection of waves */
           }
 #ifdef windows        }
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        for(i=iagemin; i <= iagemax+3; i++){  
      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);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
 #endif            posprop += prop[jk][i]; 
 #ifdef unix          } 
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);          for(jk=1; jk <=nlstate ; jk++){     
 #endif            if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
 for (i=1; i<= nlstate ; i ++) {                probs[i][jk][j1]= prop[jk][i]/posprop;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              } else{
   else fprintf(ficgp," \%%*lf (\%%*lf)");                if(first==1){
 }                  first=0;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);                  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]);
     for (i=1; i<= nlstate ; i ++) {                }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              }
   else fprintf(ficgp," \%%*lf (\%%*lf)");            } 
 }          }/* end jk */ 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        }/* end i */ 
      for (i=1; i<= nlstate ; i ++) {      /*} *//* end i1 */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    } /* end j1 */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    
 }      /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    /*free_vector(pp,1,nlstate);*/
 #ifdef unix    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");  }  /* End of prevalence */
 #endif  
    }  /************* Waves Concatenation ***************/
   }  
   /*2 eme*/  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   {
   for (k1=1; k1<= m ; k1 ++) {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);       Death is a valid wave (if date is known).
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     for (i=1; i<= nlstate+1 ; i ++) {       and mw[mi+1][i]. dh depends on stepm.
       k=2*i;       */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {    int i, mi, m;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");       double sum=0., jmean=0.;*/
 }      int first;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    int j, k=0,jk, ju, jl;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    double sum=0.;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    first=0;
       for (j=1; j<= nlstate+1 ; j ++) {    jmin=1e+5;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    jmax=-1;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    jmean=0.;
 }      for(i=1; i<=imx; i++){
       fprintf(ficgp,"\" t\"\" w l 0,");      mi=0;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      m=firstpass;
       for (j=1; j<= nlstate+1 ; j ++) {      while(s[m][i] <= nlstate){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          mw[++mi][i]=m;
 }          if(m >=lastpass)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          break;
       else fprintf(ficgp,"\" t\"\" w l 0,");        else
     }          m++;
   }      }/* end while */
        if (s[m][i] > nlstate){
   /*3eme*/        mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
   for (k1=1; k1<= m ; k1 ++) {           /* Only death is a correct wave */
     for (cpt=1; cpt<= nlstate ; cpt ++) {        mw[mi][i]=m;
       k=2+nlstate*(2*cpt-2);      }
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);      wav[i]=mi;
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      if(mi==0){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        nbwarn++;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        if(first==0){
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          first=1;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        }
         if(first==1){
 */          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       for (i=1; i< nlstate ; i ++) {        }
         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);      } /* end mi==0 */
     } /* End individuals */
       }  
     }    for(i=1; i<=imx; i++){
   }      for(mi=1; mi<wav[i];mi++){
          if (stepm <=0)
   /* CV preval stat */          dh[mi][i]=1;
     for (k1=1; k1<= m ; k1 ++) {        else{
     for (cpt=1; cpt<nlstate ; cpt ++) {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       k=3;            if (agedc[i] < 2*AGESUP) {
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);              if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
       for (i=1; i< nlstate ; i ++)                nberr++;
         fprintf(ficgp,"+$%d",k+i+1);                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]);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                j=1; /* Temporary Dangerous patch */
                      printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       l=3+(nlstate+ndeath)*cpt;                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       for (i=1; i< nlstate ; i ++) {              }
         l=3+(nlstate+ndeath)*cpt;              k=k+1;
         fprintf(ficgp,"+$%d",l+i+1);              if (j >= jmax){
       }                jmax=j;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                  ijmax=i;
     }              }
   }                if (j <= jmin){
                  jmin=j;
   /* proba elementaires */                ijmin=i;
    for(i=1,jk=1; i <=nlstate; i++){              }
     for(k=1; k <=(nlstate+ndeath); k++){              sum=sum+j;
       if (k != i) {              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         for(j=1; j <=ncovmodel; j++){              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            }
           jk++;          }
           fprintf(ficgp,"\n");          else{
         }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       }  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
     }  
    }            k=k+1;
             if (j >= jmax) {
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/              jmax=j;
      for(jk=1; jk <=m; jk++) {              ijmax=i;
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);            }
        if (ng==2)            else if (j <= jmin){
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");              jmin=j;
        else              ijmin=i;
          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 (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
        i=1;            /*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]);*/
        for(k2=1; k2<=nlstate; k2++) {            if(j<0){
          k3=i;              nberr++;
          for(k=1; k<=(nlstate+ndeath); k++) {              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]);
            if (k != k2){              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(ng==2)            }
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);            sum=sum+j;
              else          }
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          jk= j/stepm;
              ij=1;          jl= j -jk*stepm;
              for(j=3; j <=ncovmodel; j++) {          ju= j -(jk+1)*stepm;
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            if(jl==0){
                  ij++;              dh[mi][i]=jk;
                }              bh[mi][i]=0;
                else            }else{ /* We want a negative bias in order to only have interpolation ie
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                    * to avoid the price of an extra matrix product in likelihood */
              }              dh[mi][i]=jk+1;
              fprintf(ficgp,")/(1");              bh[mi][i]=ju;
                          }
              for(k1=1; k1 <=nlstate; k1++){            }else{
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            if(jl <= -ju){
                ij=1;              dh[mi][i]=jk;
                for(j=3; j <=ncovmodel; j++){              bh[mi][i]=jl;       /* bias is positive if real duration
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                                   * is higher than the multiple of stepm and negative otherwise.
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                                   */
                    ij++;            }
                  }            else{
                  else              dh[mi][i]=jk+1;
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              bh[mi][i]=ju;
                }            }
                fprintf(ficgp,")");            if(dh[mi][i]==0){
              }              dh[mi][i]=1; /* At least one step */
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);              bh[mi][i]=ju; /* At least one step */
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");              /*  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);*/
              i=i+ncovmodel;            }
            }          } /* end if mle */
          } /* end k */        }
        } /* end k2 */      } /* end wave */
      } /* end jk */    }
    } /* end ng */    jmean=sum/k;
    fclose(ficgp);    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);
 }  /* end gnuplot */    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);
    }
   
 /*************** Moving average **************/  /*********** Tricode ****************************/
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   {
   int i, cpt, cptcod;    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
       for (i=1; i<=nlstate;i++)    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
           mobaverage[(int)agedeb][i][cptcod]=0.;    /* nbcode[Tvar[j]][1]= 
        */
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){  
       for (i=1; i<=nlstate;i++){    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    int modmaxcovj=0; /* Modality max of covariates j */
           for (cpt=0;cpt<=4;cpt++){    int cptcode=0; /* Modality max of covariates j */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    int modmincovj=0; /* Modality min of covariates j */
           }  
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  
         }    cptcoveff=0; 
       }   
     }    for (k=-1; k < maxncov; k++) Ndum[k]=0;
        for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
 }  
     /* Loop on covariates without age and products */
     for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
 /************** Forecasting ******************/      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
 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){                                 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
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                                      * If product of Vn*Vm, still boolean *:
   int *popage;                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
   double *popeffectif,*popcount;        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
   double ***p3mat;                                        modality of the nth covariate of individual i. */
   char fileresf[FILENAMELENGTH];        if (ij > modmaxcovj)
           modmaxcovj=ij; 
  agelim=AGESUP;        else if (ij < modmincovj) 
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          modmincovj=ij; 
         if ((ij < -1) && (ij > NCOVMAX)){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
            exit(1);
          }else
   strcpy(fileresf,"f");        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
   strcat(fileresf,fileres);        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   if((ficresf=fopen(fileresf,"w"))==NULL) {        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     printf("Problem with forecast resultfile: %s\n", fileresf);        /* getting the maximum value of the modality of the covariate
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
   }           female is 1, then modmaxcovj=1.*/
   printf("Computing forecasting: result on file '%s' \n", fileresf);      }
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       cptcode=modmaxcovj;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
      /*for (i=0; i<=cptcode; i++) {*/
   if (mobilav==1) {      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
     movingaverage(agedeb, fage, ageminpar, mobaverage);        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
   }          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
         }
   stepsize=(int) (stepm+YEARM-1)/YEARM;        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
   if (stepm<=12) stepsize=1;           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
        } /* Ndum[-1] number of undefined modalities */
   agelim=AGESUP;  
        /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
   hstepm=1;      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
   hstepm=hstepm/stepm;      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
   yp1=modf(dateintmean,&yp);         modmincovj=3; modmaxcovj = 7;
   anprojmean=yp;         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
   yp2=modf((yp1*12),&yp);         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
   mprojmean=yp;         variables V1_1 and V1_2.
   yp1=modf((yp2*30.5),&yp);         nbcode[Tvar[j]][ij]=k;
   jprojmean=yp;         nbcode[Tvar[j]][1]=0;
   if(jprojmean==0) jprojmean=1;         nbcode[Tvar[j]][2]=1;
   if(mprojmean==0) jprojmean=1;         nbcode[Tvar[j]][3]=2;
        */
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      ij=1; /* ij is similar to i but can jumps over null modalities */
        for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
   for(cptcov=1;cptcov<=i2;cptcov++){        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          /*recode from 0 */
       k=k+1;          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
       fprintf(ficresf,"\n#******");            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
       for(j=1;j<=cptcoveff;j++) {                                       k is a modality. If we have model=V1+V1*sex 
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
       }            ij++;
       fprintf(ficresf,"******\n");          }
       fprintf(ficresf,"# StartingAge FinalAge");          if (ij > ncodemax[j]) break; 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        }  /* end of loop on */
            } /* end of loop on modality */ 
          } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    
         fprintf(ficresf,"\n");   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      
     for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
           nhstepm = nhstepm/hstepm;     Ndum[ij]++; 
             } 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;   ij=1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);     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]);*/
           for (h=0; h<=nhstepm; h++){     if((Ndum[i]!=0) && (i<=ncovcol)){
             if (h==(int) (calagedate+YEARM*cpt)) {       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);       Tvaraff[ij]=i; /*For printing (unclear) */
             }       ij++;
             for(j=1; j<=nlstate+ndeath;j++) {     }else
               kk1=0.;kk2=0;         Tvaraff[ij]=0;
               for(i=1; i<=nlstate;i++) {                 }
                 if (mobilav==1)   ij--;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];   cptcoveff=ij; /*Number of total covariates*/
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  }
                 }  
                  
               }  /*********** Health Expectancies ****************/
               if (h==(int)(calagedate+12*cpt)){  
                 fprintf(ficresf," %.3f", kk1);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
                          
               }  {
             }    /* Health expectancies, no variances */
           }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int nhstepma, nstepma; /* Decreasing with age */
         }    double age, agelim, hf;
       }    double ***p3mat;
     }    double eip;
   }  
            pstamp(ficreseij);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     fprintf(ficreseij,"# Age");
   fclose(ficresf);    for(i=1; i<=nlstate;i++){
 }      for(j=1; j<=nlstate;j++){
 /************** Forecasting ******************/        fprintf(ficreseij," e%1d%1d ",i,j);
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){      }
        fprintf(ficreseij," e%1d. ",i);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    }
   int *popage;    fprintf(ficreseij,"\n");
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;    
   double ***p3mat,***tabpop,***tabpopprev;    if(estepm < stepm){
   char filerespop[FILENAMELENGTH];      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    else  hstepm=estepm;   
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* We compute the life expectancy from trapezoids spaced every estepm months
   agelim=AGESUP;     * This is mainly to measure the difference between two models: for example
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;     * if stepm=24 months pijx are given only every 2 years and by summing them
       * we are calculating an estimate of the Life Expectancy assuming a linear 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);     * 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
   strcpy(filerespop,"pop");     * to compare the new estimate of Life expectancy with the same linear 
   strcat(filerespop,fileres);     * hypothesis. A more precise result, taking into account a more precise
   if((ficrespop=fopen(filerespop,"w"))==NULL) {     * curvature will be obtained if estepm is as small as stepm. */
     printf("Problem with forecast resultfile: %s\n", filerespop);  
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);    /* For example we decided to compute the life expectancy with the smallest unit */
   }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   printf("Computing forecasting: result on file '%s' \n", filerespop);       nhstepm is the number of hstepm from age to agelim 
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   if (cptcoveff==0) ncodemax[cptcoveff]=1;       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   if (mobilav==1) {       survival function given by stepm (the optimization length). Unfortunately it
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       means that if the survival funtion is printed only each two years of age and if
     movingaverage(agedeb, fage, ageminpar, mobaverage);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   }       results. So we changed our mind and took the option of the best precision.
     */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   if (stepm<=12) stepsize=1;  
      agelim=AGESUP;
   agelim=AGESUP;    /* If stepm=6 months */
        /* Computed by stepm unit matrices, product of hstepm matrices, stored
   hstepm=1;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   hstepm=hstepm/stepm;      
    /* nhstepm age range expressed in number of stepm */
   if (popforecast==1) {    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     if((ficpop=fopen(popfile,"r"))==NULL) {    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       printf("Problem with population file : %s\n",popfile);exit(0);    /* if (stepm >= YEARM) hstepm=1;*/
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     }    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);    for (age=bage; age<=fage; age ++){ 
     popcount=vector(0,AGESUP);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
          /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     i=1;        /* if (stepm >= YEARM) hstepm=1;*/
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
      
     imx=i;      /* If stepm=6 months */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   }         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
   for(cptcov=1;cptcov<=i2;cptcov++){      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      
       k=k+1;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       fprintf(ficrespop,"\n#******");      
       for(j=1;j<=cptcoveff;j++) {      printf("%d|",(int)age);fflush(stdout);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       }      
       fprintf(ficrespop,"******\n");      /* Computing expectancies */
       fprintf(ficrespop,"# Age");      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);        for(j=1; j<=nlstate;j++)
       if (popforecast==1)  fprintf(ficrespop," [Population]");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                  eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       for (cpt=0; cpt<=0;cpt++) {            
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              /* 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 (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;      fprintf(ficreseij,"%3.0f",age );
                for(i=1; i<=nlstate;i++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        eip=0;
           oldm=oldms;savm=savms;        for(j=1; j<=nlstate;j++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            eip +=eij[i][j][(int)age];
                  fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
           for (h=0; h<=nhstepm; h++){        }
             if (h==(int) (calagedate+YEARM*cpt)) {        fprintf(ficreseij,"%9.4f", eip );
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      }
             }      fprintf(ficreseij,"\n");
             for(j=1; j<=nlstate+ndeath;j++) {      
               kk1=0.;kk2=0;    }
               for(i=1; i<=nlstate;i++) {                  free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                 if (mobilav==1)    printf("\n");
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    fprintf(ficlog,"\n");
                 else {    
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  }
                 }  
               }  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[] )
               if (h==(int)(calagedate+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  {
                   /*fprintf(ficrespop," %.3f", kk1);    /* Covariances of health expectancies eij and of total life expectancies according
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/     to initial status i, ei. .
               }    */
             }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
             for(i=1; i<=nlstate;i++){    int nhstepma, nstepma; /* Decreasing with age */
               kk1=0.;    double age, agelim, hf;
                 for(j=1; j<=nlstate;j++){    double ***p3matp, ***p3matm, ***varhe;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    double **dnewm,**doldm;
                 }    double *xp, *xm;
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    double **gp, **gm;
             }    double ***gradg, ***trgradg;
     int theta;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)  
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    double eip, vip;
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         }    xp=vector(1,npar);
       }    xm=vector(1,npar);
      dnewm=matrix(1,nlstate*nlstate,1,npar);
   /******/    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    pstamp(ficresstdeij);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(ficresstdeij,"# Age");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    for(i=1; i<=nlstate;i++){
           nhstepm = nhstepm/hstepm;      for(j=1; j<=nlstate;j++)
                  fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficresstdeij," e%1d. ",i);
           oldm=oldms;savm=savms;    }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficresstdeij,"\n");
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    pstamp(ficrescveij);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
             }    fprintf(ficrescveij,"# Age");
             for(j=1; j<=nlstate+ndeath;j++) {    for(i=1; i<=nlstate;i++)
               kk1=0.;kk2=0;      for(j=1; j<=nlstate;j++){
               for(i=1; i<=nlstate;i++) {                      cptj= (j-1)*nlstate+i;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            for(i2=1; i2<=nlstate;i2++)
               }          for(j2=1; j2<=nlstate;j2++){
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);            cptj2= (j2-1)*nlstate+i2;
             }            if(cptj2 <= cptj)
           }              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
         }      }
       }    fprintf(ficrescveij,"\n");
    }    
   }    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
     else  hstepm=estepm;   
   if (popforecast==1) {    /* We compute the life expectancy from trapezoids spaced every estepm months
     free_ivector(popage,0,AGESUP);     * This is mainly to measure the difference between two models: for example
     free_vector(popeffectif,0,AGESUP);     * if stepm=24 months pijx are given only every 2 years and by summing them
     free_vector(popcount,0,AGESUP);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   }     * progression in between and thus overestimating or underestimating according
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * to the curvature of the survival function. If, for the same date, we 
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   fclose(ficrespop);     * 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. */
 /***********************************************/  
 /**************** Main Program *****************/    /* 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 main(int argc, char *argv[])       nstepm is the number of stepm from age to agelin. 
 {       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   double agedeb, agefin,hf;       survival function given by stepm (the optimization length). Unfortunately it
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;       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 fret;       results. So we changed our mind and took the option of the best precision.
   double **xi,tmp,delta;    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double dum; /* Dummy variable */  
   double ***p3mat;    /* If stepm=6 months */
   int *indx;    /* nhstepm age range expressed in number of stepm */
   char line[MAXLINE], linepar[MAXLINE];    agelim=AGESUP;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
   int firstobs=1, lastobs=10;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   int sdeb, sfin; /* Status at beginning and end */    /* if (stepm >= YEARM) hstepm=1;*/
   int c,  h , cpt,l;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   int ju,jl, mi;    
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   int mobilav=0,popforecast=0;    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   int hstepm, nhstepm;    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   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;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      /* Computing  Variances of health expectancies */
        /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
   char *alph[]={"a","a","b","c","d","e"}, str[4];      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   char z[1]="c", occ;          xm[i] = x[i] - (i==theta ?delti[theta]:0);
 #include <sys/time.h>        }
 #include <time.h>        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
      
   /* long total_usecs;        for(j=1; j<= nlstate; j++){
   struct timeval start_time, end_time;          for(i=1; i<=nlstate; i++){
              for(h=0; h<=nhstepm-1; h++){
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
   getcwd(pathcd, size);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
   printf("\n%s",version);          }
   if(argc <=1){        }
     printf("\nEnter the parameter file name: ");       
     scanf("%s",pathtot);        for(ij=1; ij<= nlstate*nlstate; ij++)
   }          for(h=0; h<=nhstepm-1; h++){
   else{            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
     strcpy(pathtot,argv[1]);          }
   }      }/* End theta */
   /*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);*/      for(h=0; h<=nhstepm-1; h++)
   /* cutv(path,optionfile,pathtot,'\\');*/        for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);            trgradg[h][j][theta]=gradg[h][theta][j];
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      
   chdir(path);  
   replace(pathc,path);       for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
 /*-------- arguments in the command line --------*/          varhe[ij][ji][(int)age] =0.;
   
   /* Log file */       printf("%d|",(int)age);fflush(stdout);
   strcat(filelog, optionfilefiname);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   strcat(filelog,".log");    /* */       for(h=0;h<=nhstepm-1;h++){
   if((ficlog=fopen(filelog,"w"))==NULL)    {        for(k=0;k<=nhstepm-1;k++){
     printf("Problem with logfile %s\n",filelog);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     goto end;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   }          for(ij=1;ij<=nlstate*nlstate;ij++)
   fprintf(ficlog,"Log filename:%s\n",filelog);            for(ji=1;ji<=nlstate*nlstate;ji++)
   fprintf(ficlog,"\n%s",version);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
   fprintf(ficlog,"\nEnter the parameter file name: ");        }
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      }
   fflush(ficlog);  
       /* Computing expectancies */
   /* */      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   strcpy(fileres,"r");      for(i=1; i<=nlstate;i++)
   strcat(fileres, optionfilefiname);        for(j=1; j<=nlstate;j++)
   strcat(fileres,".txt");    /* Other files have txt extension */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   /*---------arguments file --------*/            
             /* 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]);*/
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  
     printf("Problem with optionfile %s\n",optionfile);          }
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);  
     goto end;      fprintf(ficresstdeij,"%3.0f",age );
   }      for(i=1; i<=nlstate;i++){
         eip=0.;
   strcpy(filereso,"o");        vip=0.;
   strcat(filereso,fileres);        for(j=1; j<=nlstate;j++){
   if((ficparo=fopen(filereso,"w"))==NULL) {          eip += eij[i][j][(int)age];
     printf("Problem with Output resultfile: %s\n", filereso);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
     goto end;          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
   }        }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   /* Reads comments: lines beginning with '#' */      }
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficresstdeij,"\n");
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      fprintf(ficrescveij,"%3.0f",age );
     puts(line);      for(i=1; i<=nlstate;i++)
     fputs(line,ficparo);        for(j=1; j<=nlstate;j++){
   }          cptj= (j-1)*nlstate+i;
   ungetc(c,ficpar);          for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
   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);              cptj2= (j2-1)*nlstate+i2;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);              if(cptj2 <= cptj)
   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(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
 while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);      fprintf(ficrescveij,"\n");
     puts(line);     
     fputs(line,ficparo);    }
   }    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   ungetc(c,ficpar);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
        free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   covar=matrix(0,NCOVMAX,1,n);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   cptcovn=0;    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    printf("\n");
     fprintf(ficlog,"\n");
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    free_vector(xm,1,npar);
      free_vector(xp,1,npar);
   /* Read guess parameters */    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   /* Reads comments: lines beginning with '#' */    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     ungetc(c,ficpar);  }
     fgets(line, MAXLINE, ficpar);  
     puts(line);  /************ Variance ******************/
     fputs(line,ficparo);  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[])
   }  {
   ungetc(c,ficpar);    /* Variance of health expectancies */
      /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    /* double **newm;*/
     for(i=1; i <=nlstate; i++)    double **dnewm,**doldm;
     for(j=1; j <=nlstate+ndeath-1; j++){    double **dnewmp,**doldmp;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    int i, j, nhstepm, hstepm, h, nstepm ;
       fprintf(ficparo,"%1d%1d",i1,j1);    int k, cptcode;
       if(mle==1)    double *xp;
         printf("%1d%1d",i,j);    double **gp, **gm;  /* for var eij */
       fprintf(ficlog,"%1d%1d",i,j);    double ***gradg, ***trgradg; /*for var eij */
       for(k=1; k<=ncovmodel;k++){    double **gradgp, **trgradgp; /* for var p point j */
         fscanf(ficpar," %lf",&param[i][j][k]);    double *gpp, *gmp; /* for var p point j */
         if(mle==1){    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           printf(" %lf",param[i][j][k]);    double ***p3mat;
           fprintf(ficlog," %lf",param[i][j][k]);    double age,agelim, hf;
         }    double ***mobaverage;
         else    int theta;
           fprintf(ficlog," %lf",param[i][j][k]);    char digit[4];
         fprintf(ficparo," %lf",param[i][j][k]);    char digitp[25];
       }  
       fscanf(ficpar,"\n");    char fileresprobmorprev[FILENAMELENGTH];
       if(mle==1)  
         printf("\n");    if(popbased==1){
       fprintf(ficlog,"\n");      if(mobilav!=0)
       fprintf(ficparo,"\n");        strcpy(digitp,"-populbased-mobilav-");
     }      else strcpy(digitp,"-populbased-nomobil-");
      }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    else 
       strcpy(digitp,"-stablbased-");
   p=param[1][1];  
      if (mobilav!=0) {
   /* Reads comments: lines beginning with '#' */      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   while((c=getc(ficpar))=='#' && c!= EOF){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     ungetc(c,ficpar);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     fgets(line, MAXLINE, ficpar);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     puts(line);      }
     fputs(line,ficparo);    }
   }  
   ungetc(c,ficpar);    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   for(i=1; i <=nlstate; i++){    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     for(j=1; j <=nlstate+ndeath-1; j++){    strcat(fileresprobmorprev,fileres);
       fscanf(ficpar,"%1d%1d",&i1,&j1);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("%1d%1d",i,j);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficparo,"%1d%1d",i1,j1);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       for(k=1; k<=ncovmodel;k++){    }
         fscanf(ficpar,"%le",&delti3[i][j][k]);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         printf(" %le",delti3[i][j][k]);   
         fprintf(ficparo," %le",delti3[i][j][k]);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       }    pstamp(ficresprobmorprev);
       fscanf(ficpar,"\n");    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
       printf("\n");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       fprintf(ficparo,"\n");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     }      fprintf(ficresprobmorprev," p.%-d SE",j);
   }      for(i=1; i<=nlstate;i++)
   delti=delti3[1][1];        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      }  
   /* Reads comments: lines beginning with '#' */    fprintf(ficresprobmorprev,"\n");
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficgp,"\n# Routine varevsij");
     ungetc(c,ficpar);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     fgets(line, MAXLINE, ficpar);    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");
     puts(line);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     fputs(line,ficparo);  /*   } */
   }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   ungetc(c,ficpar);    pstamp(ficresvij);
      fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
   matcov=matrix(1,npar,1,npar);    if(popbased==1)
   for(i=1; i <=npar; i++){      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);
     fscanf(ficpar,"%s",&str);    else
     if(mle==1)      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
       printf("%s",str);    fprintf(ficresvij,"# Age");
     fprintf(ficlog,"%s",str);    for(i=1; i<=nlstate;i++)
     fprintf(ficparo,"%s",str);      for(j=1; j<=nlstate;j++)
     for(j=1; j <=i; j++){        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
       fscanf(ficpar," %le",&matcov[i][j]);    fprintf(ficresvij,"\n");
       if(mle==1){  
         printf(" %.5le",matcov[i][j]);    xp=vector(1,npar);
         fprintf(ficlog," %.5le",matcov[i][j]);    dnewm=matrix(1,nlstate,1,npar);
       }    doldm=matrix(1,nlstate,1,nlstate);
       else    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
         fprintf(ficlog," %.5le",matcov[i][j]);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       fprintf(ficparo," %.5le",matcov[i][j]);  
     }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     fscanf(ficpar,"\n");    gpp=vector(nlstate+1,nlstate+ndeath);
     if(mle==1)    gmp=vector(nlstate+1,nlstate+ndeath);
       printf("\n");    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficlog,"\n");    
     fprintf(ficparo,"\n");    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
   for(i=1; i <=npar; i++)    }
     for(j=i+1;j<=npar;j++)    else  hstepm=estepm;   
       matcov[i][j]=matcov[j][i];    /* 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. 
   if(mle==1)       nhstepm is the number of hstepm from age to agelim 
     printf("\n");       nstepm is the number of stepm from age to agelin. 
   fprintf(ficlog,"\n");       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
        survival function given by stepm (the optimization length). Unfortunately it
     /*-------- Rewriting paramater file ----------*/       means that if the survival funtion is printed every two years of age and if
      strcpy(rfileres,"r");    /* "Rparameterfile */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/       results. So we changed our mind and took the option of the best precision.
      strcat(rfileres,".");    /* */    */
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     if((ficres =fopen(rfileres,"w"))==NULL) {    agelim = AGESUP;
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     fprintf(ficres,"#%s\n",version);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     /*-------- data file ----------*/      gp=matrix(0,nhstepm,1,nlstate);
     if((fic=fopen(datafile,"r"))==NULL)    {      gm=matrix(0,nhstepm,1,nlstate);
       printf("Problem with datafile: %s\n", datafile);goto end;  
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;  
     }      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     n= lastobs;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     severity = vector(1,maxwav);        }
     outcome=imatrix(1,maxwav+1,1,n);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     num=ivector(1,n);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     moisnais=vector(1,n);  
     annais=vector(1,n);        if (popbased==1) {
     moisdc=vector(1,n);          if(mobilav ==0){
     andc=vector(1,n);            for(i=1; i<=nlstate;i++)
     agedc=vector(1,n);              prlim[i][i]=probs[(int)age][i][ij];
     cod=ivector(1,n);          }else{ /* mobilav */ 
     weight=vector(1,n);            for(i=1; i<=nlstate;i++)
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */              prlim[i][i]=mobaverage[(int)age][i][ij];
     mint=matrix(1,maxwav,1,n);          }
     anint=matrix(1,maxwav,1,n);        }
     s=imatrix(1,maxwav+1,1,n);    
     adl=imatrix(1,maxwav+1,1,n);            for(j=1; j<= nlstate; j++){
     tab=ivector(1,NCOVMAX);          for(h=0; h<=nhstepm; h++){
     ncodemax=ivector(1,8);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     i=1;          }
     while (fgets(line, MAXLINE, fic) != NULL)    {        }
       if ((i >= firstobs) && (i <=lastobs)) {        /* This for computing probability of death (h=1 means
                   computed over hstepm matrices product = hstepm*stepm months) 
         for (j=maxwav;j>=1;j--){           as a weighted average of prlim.
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        */
           strcpy(line,stra);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }        }    
                /* end probability of death */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        if (popbased==1) {
         for (j=ncovcol;j>=1;j--){          if(mobilav ==0){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            for(i=1; i<=nlstate;i++)
         }              prlim[i][i]=probs[(int)age][i][ij];
         num[i]=atol(stra);          }else{ /* mobilav */ 
                    for(i=1; i<=nlstate;i++)
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){              prlim[i][i]=mobaverage[(int)age][i][ij];
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/          }
         }
         i=i+1;  
       }        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
     }          for(h=0; h<=nhstepm; h++){
     /* printf("ii=%d", ij);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
        scanf("%d",i);*/              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   imx=i-1; /* Number of individuals */          }
         }
   /* for (i=1; i<=imx; i++){        /* This for computing probability of death (h=1 means
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;           computed over hstepm matrices product = hstepm*stepm months) 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;           as a weighted average of prlim.
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        */
     }*/        for(j=nlstate+1;j<=nlstate+ndeath;j++){
    /*  for (i=1; i<=imx; i++){          for(i=1,gmp[j]=0.; i<= nlstate; i++)
      if (s[4][i]==9)  s[4][i]=-1;           gmp[j] += prlim[i][i]*p3mat[i][j][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]));}*/        }    
          /* end probability of death */
    
   /* Calculation of the number of parameter from char model*/        for(j=1; j<= nlstate; j++) /* vareij */
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */          for(h=0; h<=nhstepm; h++){
   Tprod=ivector(1,15);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   Tvaraff=ivector(1,15);          }
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);              for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
              gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   if (strlen(model) >1){        }
     j=0, j1=0, k1=1, k2=1;  
     j=nbocc(model,'+');      } /* End theta */
     j1=nbocc(model,'*');  
     cptcovn=j+1;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     cptcovprod=j1;  
          for(h=0; h<=nhstepm; h++) /* veij */
     strcpy(modelsav,model);        for(j=1; j<=nlstate;j++)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          for(theta=1; theta <=npar; theta++)
       printf("Error. Non available option model=%s ",model);            trgradg[h][j][theta]=gradg[h][theta][j];
       fprintf(ficlog,"Error. Non available option model=%s ",model);  
       goto end;      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     }        for(theta=1; theta <=npar; theta++)
              trgradgp[j][theta]=gradgp[theta][j];
     for(i=(j+1); i>=1;i--){    
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */  
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      for(i=1;i<=nlstate;i++)
       /*scanf("%d",i);*/        for(j=1;j<=nlstate;j++)
       if (strchr(strb,'*')) {  /* Model includes a product */          vareij[i][j][(int)age] =0.;
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/  
         if (strcmp(strc,"age")==0) { /* Vn*age */      for(h=0;h<=nhstepm;h++){
           cptcovprod--;        for(k=0;k<=nhstepm;k++){
           cutv(strb,stre,strd,'V');          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           cptcovage++;          for(i=1;i<=nlstate;i++)
             Tage[cptcovage]=i;            for(j=1;j<=nlstate;j++)
             /*printf("stre=%s ", stre);*/              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }        }
         else if (strcmp(strd,"age")==0) { /* or age*Vn */      }
           cptcovprod--;    
           cutv(strb,stre,strc,'V');      /* pptj */
           Tvar[i]=atoi(stre);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
           cptcovage++;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           Tage[cptcovage]=i;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         else {  /* Age is not in the model */          varppt[j][i]=doldmp[j][i];
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/      /* end ppptj */
           Tvar[i]=ncovcol+k1;      /*  x centered again */
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
           Tprod[k1]=i;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           Tvard[k1][1]=atoi(strc); /* m*/   
           Tvard[k1][2]=atoi(stre); /* n */      if (popbased==1) {
           Tvar[cptcovn+k2]=Tvard[k1][1];        if(mobilav ==0){
           Tvar[cptcovn+k2+1]=Tvard[k1][2];          for(i=1; i<=nlstate;i++)
           for (k=1; k<=lastobs;k++)            prlim[i][i]=probs[(int)age][i][ij];
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        }else{ /* mobilav */ 
           k1++;          for(i=1; i<=nlstate;i++)
           k2=k2+2;            prlim[i][i]=mobaverage[(int)age][i][ij];
         }        }
       }      }
       else { /* no more sum */               
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      /* This for computing probability of death (h=1 means
        /*  scanf("%d",i);*/         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       cutv(strd,strc,strb,'V');         as a weighted average of prlim.
       Tvar[i]=atoi(strc);      */
       }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       strcpy(modelsav,stra);          for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
         scanf("%d",i);*/      }    
     } /* end of loop + */      /* end probability of death */
   } /* end model */  
        fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   printf("cptcovprod=%d ", cptcovprod);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);        for(i=1; i<=nlstate;i++){
   scanf("%d ",i);*/          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     fclose(fic);        }
       } 
     /*  if(mle==1){*/      fprintf(ficresprobmorprev,"\n");
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;      fprintf(ficresvij,"%.0f ",age );
     }      for(i=1; i<=nlstate;i++)
     /*-calculation of age at interview from date of interview and age at death -*/        for(j=1; j<=nlstate;j++){
     agev=matrix(1,maxwav,1,imx);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
     for (i=1; i<=imx; i++) {      fprintf(ficresvij,"\n");
       for(m=2; (m<= maxwav); m++) {      free_matrix(gp,0,nhstepm,1,nlstate);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      free_matrix(gm,0,nhstepm,1,nlstate);
          anint[m][i]=9999;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
          s[m][i]=-1;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
        }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    } /* End age */
       }    free_vector(gpp,nlstate+1,nlstate+ndeath);
     }    free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     for (i=1; i<=imx; i++)  {    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
       for(m=1; (m<= maxwav); m++){    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
         if(s[m][i] >0){    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
           if (s[m][i] >= nlstate+1) {  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
             if(agedc[i]>0)  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
               if(moisdc[i]!=99 && andc[i]!=9999)  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
                 agev[m][i]=agedc[i];    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
            else {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
               if (andc[i]!=9999){    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
               agev[m][i]=-1;  */
               }  /*   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);
           }  
           else if(s[m][i] !=9){ /* Should no more exist */    free_vector(xp,1,npar);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    free_matrix(doldm,1,nlstate,1,nlstate);
             if(mint[m][i]==99 || anint[m][i]==9999)    free_matrix(dnewm,1,nlstate,1,npar);
               agev[m][i]=1;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             else if(agev[m][i] <agemin){    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
               agemin=agev[m][i];    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             }    fclose(ficresprobmorprev);
             else if(agev[m][i] >agemax){    fflush(ficgp);
               agemax=agev[m][i];    fflush(fichtm); 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  }  /* end varevsij */
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/  /************ Variance of prevlim ******************/
             /*   agev[m][i] = age[i]+2*m;*/  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[])
           }  {
           else { /* =9 */    /* Variance of prevalence limit */
             agev[m][i]=1;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
             s[m][i]=-1;    double **newm;
           }    double **dnewm,**doldm;
         }    int i, j, nhstepm, hstepm;
         else /*= 0 Unknown */    int k, cptcode;
           agev[m][i]=1;    double *xp;
       }    double *gp, *gm;
        double **gradg, **trgradg;
     }    double age,agelim;
     for (i=1; i<=imx; i++)  {    int theta;
       for(m=1; (m<= maxwav); m++){    
         if (s[m][i] > (nlstate+ndeath)) {    pstamp(ficresvpl);
           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(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
           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);      fprintf(ficresvpl,"# Age");
           goto end;    for(i=1; i<=nlstate;i++)
         }        fprintf(ficresvpl," %1d-%1d",i,i);
       }    fprintf(ficresvpl,"\n");
     }  
     xp=vector(1,npar);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    dnewm=matrix(1,nlstate,1,npar);
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    doldm=matrix(1,nlstate,1,nlstate);
     
     free_vector(severity,1,maxwav);    hstepm=1*YEARM; /* Every year of age */
     free_imatrix(outcome,1,maxwav+1,1,n);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     free_vector(moisnais,1,n);    agelim = AGESUP;
     free_vector(annais,1,n);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     /* free_matrix(mint,1,maxwav,1,n);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
        free_matrix(anint,1,maxwav,1,n);*/      if (stepm >= YEARM) hstepm=1;
     free_vector(moisdc,1,n);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     free_vector(andc,1,n);      gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
          gm=vector(1,nlstate);
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      for(theta=1; theta <=npar; theta++){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        for(i=1; i<=npar; i++){ /* Computes gradient */
              xp[i] = x[i] + (i==theta ?delti[theta]:0);
     /* Concatenates waves */        }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       Tcode=ivector(1,100);      
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        for(i=1; i<=npar; i++) /* Computes gradient */
       ncodemax[1]=1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
              for(i=1;i<=nlstate;i++)
    codtab=imatrix(1,100,1,10);          gm[i] = prlim[i][i];
    h=0;  
    m=pow(2,cptcoveff);        for(i=1;i<=nlstate;i++)
            gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
    for(k=1;k<=cptcoveff; k++){      } /* End theta */
      for(i=1; i <=(m/pow(2,k));i++){  
        for(j=1; j <= ncodemax[k]; j++){      trgradg =matrix(1,nlstate,1,npar);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  
            h++;      for(j=1; j<=nlstate;j++)
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;        for(theta=1; theta <=npar; theta++)
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/          trgradg[j][theta]=gradg[theta][j];
          }  
        }      for(i=1;i<=nlstate;i++)
      }        varpl[i][(int)age] =0.;
    }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       codtab[1][2]=1;codtab[2][2]=2; */      for(i=1;i<=nlstate;i++)
    /* for(i=1; i <=m ;i++){        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
       for(k=1; k <=cptcovn; k++){  
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);      fprintf(ficresvpl,"%.0f ",age );
       }      for(i=1; i<=nlstate;i++)
       printf("\n");        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       }      fprintf(ficresvpl,"\n");
       scanf("%d",i);*/      free_vector(gp,1,nlstate);
          free_vector(gm,1,nlstate);
    /* Calculates basic frequencies. Computes observed prevalence at single age      free_matrix(gradg,1,npar,1,nlstate);
        and prints on file fileres'p'. */      free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
      
        free_vector(xp,1,npar);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_matrix(doldm,1,nlstate,1,npar);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_matrix(dnewm,1,nlstate,1,nlstate);
     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 */  
        /************ Variance of one-step probabilities  ******************/
     /* For Powell, parameters are in a vector p[] starting at p[1]  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[])
        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) */    int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     if(mle==1){    int k=0,l, cptcode;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    int first=1, first1, first2;
     }    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
        double **dnewm,**doldm;
     /*--------- results files --------------*/    double *xp;
     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);    double *gp, *gm;
      double **gradg, **trgradg;
     double **mu;
    jk=1;    double age,agelim, cov[NCOVMAX+1];
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    int theta;
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    char fileresprob[FILENAMELENGTH];
    for(i=1,jk=1; i <=nlstate; i++){    char fileresprobcov[FILENAMELENGTH];
      for(k=1; k <=(nlstate+ndeath); k++){    char fileresprobcor[FILENAMELENGTH];
        if (k != i)    double ***varpij;
          {  
            printf("%d%d ",i,k);    strcpy(fileresprob,"prob"); 
            fprintf(ficlog,"%d%d ",i,k);    strcat(fileresprob,fileres);
            fprintf(ficres,"%1d%1d ",i,k);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
            for(j=1; j <=ncovmodel; j++){      printf("Problem with resultfile: %s\n", fileresprob);
              printf("%f ",p[jk]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
              fprintf(ficlog,"%f ",p[jk]);    }
              fprintf(ficres,"%f ",p[jk]);    strcpy(fileresprobcov,"probcov"); 
              jk++;    strcat(fileresprobcov,fileres);
            }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
            printf("\n");      printf("Problem with resultfile: %s\n", fileresprobcov);
            fprintf(ficlog,"\n");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
            fprintf(ficres,"\n");    }
          }    strcpy(fileresprobcor,"probcor"); 
      }    strcat(fileresprobcor,fileres);
    }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
    if(mle==1){      printf("Problem with resultfile: %s\n", fileresprobcor);
      /* Computing hessian and covariance matrix */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
      ftolhess=ftol; /* Usually correct */    }
      hesscov(matcov, p, npar, delti, ftolhess, func);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
    }    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
    printf("# Scales (for hessian or gradient estimation)\n");    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
    for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      for(j=1; j <=nlstate+ndeath; j++){    pstamp(ficresprob);
        if (j!=i) {    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
          fprintf(ficres,"%1d%1d",i,j);    fprintf(ficresprob,"# Age");
          printf("%1d%1d",i,j);    pstamp(ficresprobcov);
          fprintf(ficlog,"%1d%1d",i,j);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
          for(k=1; k<=ncovmodel;k++){    fprintf(ficresprobcov,"# Age");
            printf(" %.5e",delti[jk]);    pstamp(ficresprobcor);
            fprintf(ficlog," %.5e",delti[jk]);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
            fprintf(ficres," %.5e",delti[jk]);    fprintf(ficresprobcor,"# Age");
            jk++;  
          }  
          printf("\n");    for(i=1; i<=nlstate;i++)
          fprintf(ficlog,"\n");      for(j=1; j<=(nlstate+ndeath);j++){
          fprintf(ficres,"\n");        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
        }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
      }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
    }      }  
       /* fprintf(ficresprob,"\n");
    k=1;    fprintf(ficresprobcov,"\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");    fprintf(ficresprobcor,"\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");    xp=vector(1,npar);
    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");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
    for(i=1;i<=npar;i++){    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      /*  if (k>nlstate) k=1;    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
          i1=(i-1)/(ncovmodel*nlstate)+1;    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    first=1;
          printf("%s%d%d",alph[k],i1,tab[i]);*/    fprintf(ficgp,"\n# Routine varprob");
      fprintf(ficres,"%3d",i);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
      if(mle==1)    fprintf(fichtm,"\n");
        printf("%3d",i);  
      fprintf(ficlog,"%3d",i);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
      for(j=1; j<=i;j++){    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
        fprintf(ficres," %.5e",matcov[i][j]);    file %s<br>\n",optionfilehtmcov);
        if(mle==1)    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
          printf(" %.5e",matcov[i][j]);  and drawn. It helps understanding how is the covariance between two incidences.\
        fprintf(ficlog," %.5e",matcov[i][j]);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
      }    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
      fprintf(ficres,"\n");  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
      if(mle==1)  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
        printf("\n");  standard deviations wide on each axis. <br>\
      fprintf(ficlog,"\n");   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
      k++;   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
    }  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
      
    while((c=getc(ficpar))=='#' && c!= EOF){    cov[1]=1;
      ungetc(c,ficpar);    /* tj=cptcoveff; */
      fgets(line, MAXLINE, ficpar);    tj = (int) pow(2,cptcoveff);
      puts(line);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
      fputs(line,ficparo);    j1=0;
    }    for(j1=1; j1<=tj;j1++){
    ungetc(c,ficpar);      /*for(i1=1; i1<=ncodemax[t];i1++){ */
    estepm=0;      /*j1++;*/
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);        if  (cptcovn>0) {
    if (estepm==0 || estepm < stepm) estepm=stepm;          fprintf(ficresprob, "\n#********** Variable "); 
    if (fage <= 2) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      bage = ageminpar;          fprintf(ficresprob, "**********\n#\n");
      fage = agemaxpar;          fprintf(ficresprobcov, "\n#********** Variable "); 
    }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              fprintf(ficresprobcov, "**********\n#\n");
    fprintf(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(ficgp, "\n#********** Variable "); 
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              fprintf(ficgp, "**********\n#\n");
    while((c=getc(ficpar))=='#' && c!= EOF){          
      ungetc(c,ficpar);          
      fgets(line, MAXLINE, ficpar);          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
      puts(line);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      fputs(line,ficparo);          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
    }          
    ungetc(c,ficpar);          fprintf(ficresprobcor, "\n#********** Variable ");    
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);          fprintf(ficresprobcor, "**********\n#");    
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        }
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        
            gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
    while((c=getc(ficpar))=='#' && c!= EOF){        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      ungetc(c,ficpar);        gp=vector(1,(nlstate)*(nlstate+ndeath));
      fgets(line, MAXLINE, ficpar);        gm=vector(1,(nlstate)*(nlstate+ndeath));
      puts(line);        for (age=bage; age<=fage; age ++){ 
      fputs(line,ficparo);          cov[2]=age;
    }          for (k=1; k<=cptcovn;k++) {
    ungetc(c,ficpar);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                             * 1  1 1 1 1
                                                            * 2  2 1 1 1
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                                                           * 3  1 2 1 1
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                                                           */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
   fscanf(ficpar,"pop_based=%d\n",&popbased);          }
   fprintf(ficparo,"pop_based=%d\n",popbased);            for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   fprintf(ficres,"pop_based=%d\n",popbased);            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]]];
   while((c=getc(ficpar))=='#' && c!= EOF){          
     ungetc(c,ficpar);      
     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]:(double)0);
   }            
   ungetc(c,ficpar);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
   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);            k=0;
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);            for(i=1; i<= (nlstate); i++){
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
 while((c=getc(ficpar))=='#' && c!= EOF){              }
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);            
     puts(line);            for(i=1; i<=npar; i++)
     fputs(line,ficparo);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   }      
   ungetc(c,ficpar);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);            for(i=1; i<=(nlstate); i++){
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);              for(j=1; j<=(nlstate+ndeath);j++){
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                k=k+1;
                 gm[k]=pmmij[i][j];
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              }
             }
 /*------------ gnuplot -------------*/       
   strcpy(optionfilegnuplot,optionfilefiname);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   strcat(optionfilegnuplot,".gp");              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          }
     printf("Problem with file %s",optionfilegnuplot);  
   }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   fclose(ficgp);            for(theta=1; theta <=npar; theta++)
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);              trgradg[j][theta]=gradg[theta][j];
 /*--------- index.htm --------*/          
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   strcpy(optionfilehtm,optionfile);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          pmij(pmmij,cov,ncovmodel,x,nlstate);
     printf("Problem with %s \n",optionfilehtm), exit(0);          
   }          k=0;
           for(i=1; i<=(nlstate); i++){
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n            for(j=1; j<=(nlstate+ndeath);j++){
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n              k=k+1;
 \n              mu[k][(int) age]=pmmij[i][j];
 Total number of observations=%d <br>\n            }
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n          }
 <hr  size=\"2\" color=\"#EC5E5E\">          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
  <ul><li><h4>Parameter files</h4>\n            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n              varpij[i][j][(int)age] = doldm[i][j];
  - Log file of the run: <a href=\"%s\">%s</a><br>\n  
  - 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);          /*printf("\n%d ",(int)age);
   fclose(fichtm);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
              }*/
 /*------------ free_vector  -------------*/  
  chdir(path);          fprintf(ficresprob,"\n%d ",(int)age);
            fprintf(ficresprobcov,"\n%d ",(int)age);
  free_ivector(wav,1,imx);          fprintf(ficresprobcor,"\n%d ",(int)age);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
  free_ivector(num,1,n);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
  free_vector(agedc,1,n);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
  /*free_matrix(covar,1,NCOVMAX,1,n);*/            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
  fclose(ficparo);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
  fclose(ficres);          }
           i=0;
           for (k=1; k<=(nlstate);k++){
   /*--------------- Prevalence limit --------------*/            for (l=1; l<=(nlstate+ndeath);l++){ 
                i++;
   strcpy(filerespl,"pl");              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   strcat(filerespl,fileres);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {              for (j=1; j<=i;j++){
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;                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 prevalence limit: result on file '%s' \n", filerespl);              }
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);            }
   fprintf(ficrespl,"#Prevalence limit\n");          }/* end of loop for state */
   fprintf(ficrespl,"#Age ");        } /* end of loop for age */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   fprintf(ficrespl,"\n");        free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   prlim=matrix(1,nlstate,1,nlstate);        free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        /* Confidence intervalle of pij  */
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        /*
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficgp,"\nunset parametric;unset label");
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   k=0;          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   agebase=ageminpar;          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);
   agelim=agemaxpar;          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   ftolpl=1.e-10;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   i1=cptcoveff;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   if (cptcovn < 1){i1=1;}        */
   
   for(cptcov=1;cptcov<=i1;cptcov++){        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        first1=1;first2=2;
         k=k+1;        for (k2=1; k2<=(nlstate);k2++){
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
         fprintf(ficrespl,"\n#******");            if(l2==k2) continue;
         printf("\n#******");            j=(k2-1)*(nlstate+ndeath)+l2;
         fprintf(ficlog,"\n#******");            for (k1=1; k1<=(nlstate);k1++){
         for(j=1;j<=cptcoveff;j++) {              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                if(l1==k1) continue;
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                i=(k1-1)*(nlstate+ndeath)+l1;
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                if(i<=j) continue;
         }                for (age=bage; age<=fage; age ++){ 
         fprintf(ficrespl,"******\n");                  if ((int)age %5==0){
         printf("******\n");                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
         fprintf(ficlog,"******\n");                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                            cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         for (age=agebase; age<=agelim; age++){                    mu1=mu[i][(int) age]/stepm*YEARM ;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                    mu2=mu[j][(int) age]/stepm*YEARM;
           fprintf(ficrespl,"%.0f",age );                    c12=cv12/sqrt(v1*v2);
           for(i=1; i<=nlstate;i++)                    /* Computing eigen value of matrix of covariance */
           fprintf(ficrespl," %.5f", prlim[i][i]);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
           fprintf(ficrespl,"\n");                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         }                    if ((lc2 <0) || (lc1 <0) ){
       }                      if(first2==1){
     }                        first1=0;
   fclose(ficrespl);                      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);
                       }
   /*------------- h Pij x at various ages ------------*/                      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 */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                      /* lc2=fabs(lc2); */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                    }
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;                    /* Eigen vectors */
   }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   printf("Computing pij: result on file '%s' \n", filerespij);                    /*v21=sqrt(1.-v11*v11); *//* error */
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);                    v21=(lc1-v1)/cv12*v11;
                      v12=-v21;
   stepsize=(int) (stepm+YEARM-1)/YEARM;                    v22=v11;
   /*if (stepm<=24) stepsize=2;*/                    tnalp=v21/v11;
                     if(first1==1){
   agelim=AGESUP;                      first1=0;
   hstepm=stepsize*YEARM; /* Every year of 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);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                    }
                     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);
   /* hstepm=1;   aff par mois*/                    /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   k=0;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   for(cptcov=1;cptcov<=i1;cptcov++){                    if(first==1){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                      first=0;
       k=k+1;                      fprintf(ficgp,"\nset parametric;unset label");
         fprintf(ficrespij,"\n#****** ");                      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);
         for(j=1;j<=cptcoveff;j++)                      fprintf(ficgp,"\nset ter png small size 320, 240");
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
         fprintf(ficrespij,"******\n");   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
          %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
           /*      nhstepm=nhstepm*YEARM; aff par mois*/                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
           oldm=oldms;savm=savms;                      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",\
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                                mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
           fprintf(ficrespij,"# Age");                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           for(i=1; i<=nlstate;i++)                    }else{
             for(j=1; j<=nlstate+ndeath;j++)                      first=0;
               fprintf(ficrespij," %1d-%1d",i,j);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
           fprintf(ficrespij,"\n");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
            for (h=0; h<=nhstepm; h++){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                      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",\
             for(i=1; i<=nlstate;i++)                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
               for(j=1; j<=nlstate+ndeath;j++)                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                    }/* if first */
             fprintf(ficrespij,"\n");                  } /* age mod 5 */
              }                } /* end loop age */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           fprintf(ficrespij,"\n");                first=1;
         }              } /*l12 */
     }            } /* k12 */
   }          } /*l1 */
         }/* k1 */
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);        /* } /* loop covariates */
     }
   fclose(ficrespij);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   /*---------- Forecasting ------------------*/    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
   if((stepm == 1) && (strcmp(model,".")==0)){    free_vector(xp,1,npar);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    fclose(ficresprob);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    fclose(ficresprobcov);
   }    fclose(ficresprobcor);
   else{    fflush(ficgp);
     erreur=108;    fflush(fichtmcov);
     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);  
   }  
    /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   /*---------- Health expectancies and variances ------------*/                    int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   strcpy(filerest,"t");                    int popforecast, int estepm ,\
   strcat(filerest,fileres);                    double jprev1, double mprev1,double anprev1, \
   if((ficrest=fopen(filerest,"w"))==NULL) {                    double jprev2, double mprev2,double anprev2){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    int jj1, k1, i1, cpt;
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;  
   }     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
   printf("Computing Total LEs with variances: file '%s' \n", filerest);     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);  </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
   strcpy(filerese,"e");             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
   strcat(filerese,fileres);     fprintf(fichtm,"\
   if((ficreseij=fopen(filerese,"w"))==NULL) {   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);     fprintf(fichtm,"\
   }   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);     fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
   strcpy(fileresv,"v");     <a href=\"%s\">%s</a> <br>\n",
   strcat(fileresv,fileres);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   if((ficresvij=fopen(fileresv,"w"))==NULL) {     fprintf(fichtm,"\
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);   - Population projections by age and states: \
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
   calagedate=-1;   m=pow(2,cptcoveff);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
   k=0;   jj1=0;
   for(cptcov=1;cptcov<=i1;cptcov++){   for(k1=1; k1<=m;k1++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     for(i1=1; i1<=ncodemax[k1];i1++){
       k=k+1;       jj1++;
       fprintf(ficrest,"\n#****** ");       if (cptcovn > 0) {
       for(j=1;j<=cptcoveff;j++)         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         for (cpt=1; cpt<=cptcoveff;cpt++) 
       fprintf(ficrest,"******\n");           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       fprintf(ficreseij,"\n#****** ");       }
       for(j=1;j<=cptcoveff;j++)       /* Pij */
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       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> \
       fprintf(ficreseij,"******\n");  <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
       fprintf(ficresvij,"\n#****** ");       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
       for(j=1;j<=cptcoveff;j++)   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> \
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
       fprintf(ficresvij,"******\n");         /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);           fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
       oldm=oldms;savm=savms;  <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);           }
         for(cpt=1; cpt<=nlstate;cpt++) {
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          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> \
       oldm=oldms;savm=savms;  <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);       }
       if(popbased==1){     } /* end i1 */
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);   }/* End k1 */
        }   fprintf(fichtm,"</ul>");
   
    
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");   fprintf(fichtm,"\
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
       fprintf(ficrest,"\n");   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
       epj=vector(1,nlstate+1);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       for(age=bage; age <=fage ;age++){           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   fprintf(fichtm,"\
         if (popbased==1) {   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           for(i=1; i<=nlstate;i++)           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
             prlim[i][i]=probs[(int)age][i][k];  
         }   fprintf(fichtm,"\
           - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
         fprintf(ficrest," %4.0f",age);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){   fprintf(fichtm,"\
           for(i=1, epj[j]=0.;i <=nlstate;i++) {   - 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): \
             epj[j] += prlim[i][i]*eij[i][j][(int)age];     <a href=\"%s\">%s</a> <br>\n</li>",
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/             estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
           }   fprintf(fichtm,"\
           epj[nlstate+1] +=epj[j];   - (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"));
         for(i=1, vepp=0.;i <=nlstate;i++)   fprintf(fichtm,"\
           for(j=1;j <=nlstate;j++)   - 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",
             vepp += vareij[i][j][(int)age];           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));   fprintf(fichtm,"\
         for(j=1;j <=nlstate;j++){   - 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",
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));           estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
         }   fprintf(fichtm,"\
         fprintf(ficrest,"\n");   - 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 */
 free_matrix(mint,1,maxwav,1,n);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
     free_vector(weight,1,n);  /*      <br>",fileres,fileres,fileres,fileres); */
   fclose(ficreseij);  /*  else  */
   fclose(ficresvij);  /*    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); */
   fclose(ficrest);   fflush(fichtm);
   fclose(ficpar);   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   free_vector(epj,1,nlstate+1);  
     m=pow(2,cptcoveff);
   /*------- Variance limit prevalence------*/     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
   strcpy(fileresvpl,"vpl");   jj1=0;
   strcat(fileresvpl,fileres);   for(k1=1; k1<=m;k1++){
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {     for(i1=1; i1<=ncodemax[k1];i1++){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);       jj1++;
     exit(0);       if (cptcovn > 0) {
   }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);         for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   k=0;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   for(cptcov=1;cptcov<=i1;cptcov++){       }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       for(cpt=1; cpt<=nlstate;cpt++) {
       k=k+1;         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
       fprintf(ficresvpl,"\n#****** ");  prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
       for(j=1;j<=cptcoveff;j++)  <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       }
       fprintf(ficresvpl,"******\n");       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) \
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  true period expectancies (those weighted with period prevalences are also\
       oldm=oldms;savm=savms;   drawn in addition to the population based expectancies computed using\
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);   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 */
   fclose(ficresvpl);   fprintf(fichtm,"</ul>");
    fflush(fichtm);
   /*---------- End : free ----------------*/  }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
    /******************* Gnuplot file **************/
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
      char dirfileres[132],optfileres[132];
      int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    int ng=0;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  /*     printf("Problem with file %s",optionfilegnuplot); */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
    /*   } */
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);    /*#ifdef windows */
   free_matrix(agev,1,maxwav,1,imx);    fprintf(ficgp,"cd \"%s\" \n",pathc);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      /*#endif */
     m=pow(2,cptcoveff);
   fprintf(fichtm,"\n</body>");  
   fclose(fichtm);    strcpy(dirfileres,optionfilefiname);
   fclose(ficgp);    strcpy(optfileres,"vpl");
     /* 1eme*/
     fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
   if(erreur >0){    for (cpt=1; cpt<= nlstate ; cpt ++) {
     printf("End of Imach with error or warning %d\n",erreur);      for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);       fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   }else{       fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
    printf("End of Imach\n");       fprintf(ficgp,"set xlabel \"Age\" \n\
    fprintf(ficlog,"End of Imach\n");  set ylabel \"Probability\" \n\
   }  set ter png small size 320, 240\n\
   printf("See log file on %s\n",filelog);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   fclose(ficlog);  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */       for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   /* 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);*/         else        fprintf(ficgp," \%%*lf (\%%*lf)");
   /*printf("Total time was %d uSec.\n", total_usecs);*/       }
   /*------ End -----------*/       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)");
  end:         else fprintf(ficgp," \%%*lf (\%%*lf)");
 #ifdef windows       } 
   /* chdir(pathcd);*/       fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
 #endif       for (i=1; i<= nlstate ; i ++) {
  /*system("wgnuplot graph.plt");*/         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
  /*system("../gp37mgw/wgnuplot graph.plt");*/         else fprintf(ficgp," \%%*lf (\%%*lf)");
  /*system("cd ../gp37mgw");*/       }  
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/       fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
  strcpy(plotcmd,GNUPLOTPROGRAM);     }
  strcat(plotcmd," ");    }
  strcat(plotcmd,optionfilegnuplot);    /*2 eme*/
  system(plotcmd);    fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
     for (k1=1; k1<= m ; k1 ++) { 
 #ifdef windows      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
   while (z[0] != 'q') {      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
     /* chdir(path); */      
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");      for (i=1; i<= nlstate+1 ; i ++) {
     scanf("%s",z);        k=2*i;
     if (z[0] == 'c') system("./imach");        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     else if (z[0] == 'e') system(optionfilehtm);        for (j=1; j<= nlstate+1 ; j ++) {
     else if (z[0] == 'g') system(plotcmd);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     else if (z[0] == 'q') exit(0);          else fprintf(ficgp," \%%*lf (\%%*lf)");
   }        }   
 #endif        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, c, cptcod, i, h, i1;
     int *popage;
     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], cc[32];
     int i,j, k, l, 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 m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     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, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     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 */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       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 i1, 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,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*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, fage, 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 kk1, kk2;
     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", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   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");
   #elsedef
       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");
   #elsedef
       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 */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     /*(void) gettimeofday(&end_time,&tzp);*/
     rend_time = time(NULL);  
     end_time = *localtime(&rend_time);
     /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   
     printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifdef _WIN32
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef __unix
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
       printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
     }
     printf(" Successful, please wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
   #ifdef __APPLE__
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
   #else
         sprintf(pplotcmd, "%s", optionfilehtm);
   #endif
         printf("Starting browser with: %s",pplotcmd);fflush(stdout);
         system(pplotcmd);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }

Removed from v.1.50  
changed lines
  Added in v.1.160


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